Reference Manager to EndNote FAQ

Converting from Reference Manager to EndNote? Here 
are some helpful tools to make it easy.

Converting your Reference Manager library to an EndNote library (YouTube)

Converting your Reference Manager library to an EndNote library (PDF)

Find your commonly used Reference Manager commands in EndNote (PDF)

Feature comparison of Reference Manager and EndNote

Frequently Asked Questions


1. What are the advantages of switching to EndNote?

Switching to EndNote opens up many new features not available in Reference Manager, but features aren’t the only advantage. EndNote’s popularity worldwide also includes multiple collaboration options. This makes it possible to work collaboratively with people both within and outside your organization. Here are some of the advantages in making the switch: Compatibility across Languages and Operating Systems

  • EndNote is Unicode-compliant, so you can work with references in non-Latin-based languages.
  • EndNote on the desktop can be used on both the Windows and Macintosh operating systems, with full file compatibility. You can install EndNote on up to three computers, so long as you are the sole user of the program.
  • EndNote online libraries can be accessed from any Internet browser.
  • References in EndNote libraries can be synchronized, allowing you to work with the same references on the desktop, online, and on the iPad.
  • EndNote has an iPad app, allowing you to work with your library anywhere you have your iPad. It even includes PDF annotation tools and can import records from online databases.


  • Library sharing allows an EndNote library to be synced and shared between up to 15 people, with each person having full read-write access to all references and attachments in the Library. Any change made to any copy of the library is automatically synced to all members of the sharing group, including the library owner.
  • Custom groups can be shared through EndNote online with EndNote users anywhere in the world. When groups are shared through EndNote online, attachments are not shared. You can specify read-only or read-write access to the record data for each individual member of the group.
  • A read-only copy of a library can be shared on a local network drive and any number of people can access it for use in Word, to search it, print it, read PDFs in it, etc., but nobody can make changes to it. Read-write libraries should not be placed on network drives. See this knowledge base article for more information.
  • A compressed library can be created using the File>Compressed Library command and distributed through email, a network drive, or a flash drive. The compressed library should be placed in the local computer location where it will be used, then opened to uncompress in that location.

PDF and Attachment Tools

  • EndNote has built-in PDF viewing and annotation tools.
  • EndNote can search the text in attached PDFs.
  • EndNote can import PDFs that are already on your computer.
  • EndNote can set a watched folder, then automatically import PDFs in that folder when EndNote starts.
  • EndNote can rename PDFs based on the contents of the record and criteria you set in the preferences, or can rename PDFs or other attachments manually through the References>File Attachments menu.
  • You can email PDFs from the EndNote PDF viewer.
  • EndNote’s Find Full Text feature can find PDFs online that match records in your library, download them, and attach them to your records.
  • Any kind of file can be attached to a record using the File Attachments field, and each record can hold up to 45 attachments.

Organization Tools

  • EndNote allows you to create groups and group sets to organize a large library by projects or categories. You can have up to 5,000 groups and 5,000 group sets in a library. Groups are organized under group sets and references are organized in groups.
  • Custom groups will sync with EndNote online and EndNote iPad. They require you to assign references to the group manually.
  • Smart groups are based on search criteria and will automatically update.
  • Combined groups let you combine or compare the contents of other groups.
  • Group sets can be assigned to projects or larger categories and can be dragged to a preferred location on the groups list.
  • EndNote lets you rate your references by 0 to 5 stars.
  • EndNote can mark references as read or unread.
  • EndNote can sort your library based on the sorting rules of multiple languages—and can do the same for bibliographies. Languages range from Chinese to Swedish.
  • EndNote’s record summaries show the date added to a library, the date last modified, which groups a record belongs to, the number of fields used, and the Web of Science times cited number.

Other Features

  • EndNote records can have up to 56 fields, compared to 37 in Reference Manager.
  • EndNote can have up to 48 reference types, compared to 35 in Reference Manager.
  • EndNote has a built-in file compression utility for creating backups or emailing libraries, with options for customizing the compressed file.
  • EndNote’s term list feature can be used to create your own custom lists and link them to the fields of your choice. You are not limited to the author, journals, and keywords lists available in Reference Manager. The medical term list contains over 14,000 journals, compared to less than 9,000 in Reference Manager.
  • The Find Reference Updates feature searches for matches to highlighted references online, then shows the found and current record side-by-side so you can update records you already have with new information.
  • EndNote can change the capitalization of selected text in your records.
  • CWYW in Word can create bibliographies at the end of chapters as well as the end of the document.
  • CWYW in Word can create bibliographies organized by subheadings, either based on reference type in the style or on-the-fly in a document.
  • EndNote allows you to create and share custom styles, filters, and even connection files as individual files. Connection files, used for Internet search in Reference Manager, all share a single configuration file in Reference Manager and so are not very portable. In EndNote, each connection file includes its own configuration information and can easily be shared.
  • EndNote’s Format Paper feature allows you to create formatted citations and bibliographies in any word processor that can create a rich text format (RTF) file.


2. What is different in CWYW in EndNote?

In general, Cite While You Write works much the same in EndNote and Reference Manager, but there are some important differences.

  • When entering search information in the Find Citation window in Reference Manager, the program searches only indexed fields, so fields such as the Notes or Abstract are not searched. EndNote searches almost all fields in this window, so Notes,Abstracts, and even page numbers will be searched to find matching citations.
  • Temporary citations are entered differently in EndNote than in Reference Manager, although the default format of {Author, Year #Record Number} looks similar. In EndNote, keep in mind the following points about temporary citations:
    • Removing the author’s name from the citation results in the author’s name being removed from the formatted citation.
    • Removing the year from the citation results in the year being removed from the formatted citation.
    • Removing both the author’s name and year, leaving only the EndNote record number in the temporary citation, hides the citation in the text completely for author-date formats. This means entering only a record number in a temporary citation will result in the citation being hidden in the paper by default, or only showing page numbers, suffix text, or prefix text if the switches for these were added to the record number.
    • The record number in EndNote is not static, it changes. This means if a record number is inserted alone in an EndNote temporary citation, even with the intent to hide the citation in the paper, it may result in a different citation being inserted than the one that originally had that record number. Record numbers may change whenever a record is synced between libraries on separate computers, copied from one library to another, or even cut and pasted within the same library. Because of this, record numbers should not be used as a permanent identifier in EndNote. If you wish to assign permanent unique identifiers, Label is a good field to use. Note that if you convert a Reference Manager database to an EndNote library, the old Reference Manager record number will be stored in the Label field.
    • In the EndNote formatting preferences, the field inserted along with the author name and year for a temporary citation can be customized. You can use the default record number (which may change), the Label field, the Accession Number field, or the Pages field. You can access these preferences by clicking Edit>Preferences>Temporary Citations in EndNote for Windows or EndNote>Preferences>Temporary Citations in EndNote for Macintosh.


3. What ways can I access my EndNote library?

If you are using EndNote Sync to synchronize references between your desktop and online, you have several choices in how you access and work with those references. Note that when using EndNote Sync, any change made in any synced library will be mirrored in all synced copies of the library.

  • You can access all your references, attachments, and maintain the same group structure using the EndNote desktop program on both the Windows and Macintosh operating systems. Through sync you can have a library that looks exactly the same on up to three desktop computers through EndNote Sync. Please note the record numbers in the library may be different and the journals term list would need to be set up for each library separately as it is not synced. Please see this knowledge base article for instructions on configuring the Journals Term List.
  • You can access all of your references and custom groups online using an Internet browser on any of your devices. Group sets, smart groups, and combined groups do not appear online, but the information about them is saved and will appear when the synced library is opened on the desktop. Term lists and the ability to edit PDFs are not available when working with a library online.
  • If you have an iPad, you can sync your references to the EndNote iPad app. Like the online library, only custom groups appear in the library on the iPad. Term lists are not available on the iPad but unlike when working online, the iPad app has very sophisticated PDF-editing capabilities.



1. What word processors are supported with EndNote?

Current compatibility information can be found here

2. What operating systems are supported with EndNote?

Current compatibility information can be found here


1. How do I convert my database?

Use the steps here:

2. How do I convert my documents?

Use the steps here:


1. Can I put libraries on network drives?

Yes, but they have to be read only for all users. Use the steps here:

2. Why can’t I put libraries in Dropbox, etc.?

3. How many databases/libraries can I have?

There is no limit on the number of EndNote libraries you can create. However, only one library can be synchronized and shared.


1. How do I get to Internet Search?

Reference Manager’s Internet Search command is called Online Search in EndNote. If you prefer to use the EndNote menus, select Tools>Online Search to enter Online Search mode. However, you can also customize the Online Search experience using the mode buttons for online search, shown below:
Windows Online Search Mode Windows Mac Online Search Mode Mac

  • The button to the left, showing three books or the monitor in the screenshot above, is the Local Library Mode. In this mode you will see all the references and groups in your library, but no Online Search groups.
  • The middle button is Online Search Mode. This turns the EndNote screen into a temporary preview library, where you can search online and examine the retrieved references outside of your permanent EndNote library. After examining the references, select (highlight) any references you want to keep and click the Copy to Local Library button (shown below) to copy the selected references to your permanent local library.
    Windows Copy to Local Library Windows Mac Copy to Local Library Mac
  • The button to the right, showing both a globe and books or the monitor and globe, is Integrated Library and Online Search Mode. In this mode you will see the references and groups in your permanent library and also the Online Search groups. There is no preview window when working in this mode, so all retrieved references will be permanently imported into your local library. This means references you do not want to keep will need to be deleted from the library.

Please note that EndNote can only search one library at a time, when searching within your own EndNote library, a library that is shared with you through EndNote Sharing, or when searching online. If you wish to search more than one library, you will need to search them one at a time.


2. How does the search work in EndNote?

Search is described here:

3. Does EndNote have saved search strategies?

Yes, and you can save search strategies for your local library more than one way.
  • To save a search strategy when searching an online library, click the Options button, then select Save Search to save your strategy. One big improvement over Reference Manager is the ability to give your search strategies long file names, making it easier to tell them apart.
  • When using the Search panel in your local library, you can also use the Options>Save Search command to save a search strategy. However, doing this means that you need to run that search every time you want to see the results. To easily see that result set at all times and to have it automatically update, use a Smart Group instead.
  • Windows Smart GroupsMac Smart Groups Smart groups are based on a search and have a light bulb icon or gear icon to the left of the group name. Smart groups are updated automatically with any reference in the library matching the group’s search criteria. Smart groups always search the entire library and can only search EndNote desktop libraries. Smart groups cannot search online libraries.
    • To create a smart group, select Create Smart Group from the Groups menu, then build your search criteria,
    • Create your search in the search panel; click Options or the gear icon on the Mac, then select Convert to Smart Group.



1. How can I use EndNote to manage my PDFs?

EndNote’s PDF handling capabilities are much more robust than Reference Manager’s. You can:

  • Attach one or more PDFs to any record. (To learn how, see )
  • Select between “relative” links, which embeds a copy of the PDF in the library’s .Data folder, or an “absolute” link, which links to a file anywhere on your local disk. (We recommend using relative links for the best compatibility with online sync and sharing, as absolute links are not shared or synced).
  • Transfer your library by sync or compressed library and, if you’ve used the relative linking function, the PDFs will go with it! (Details on using Sync can be found here: )
  • Import PDFs that have registered DOIs to automatically have EndNote create a new record with the PDF attached. You can even import an entire folder of PDFs at once! (Details on importing PDF Folders or files can be found here )
  • Use EndNote’s library search to search within your attached full-text PDFs.
  • Use Find Full Text to automatically search for freely available PDFs of your references. (Learn more about the Find Full Text feature here: )
  • Built-in annotation tools allow you to add highlighting and comments into any attached full-text PDF. (Learn how here: )


2. Where is my attachments folder?

By default, EndNote will store a copy of any attached PDFs within the library’s .Data folder. Look for this folder in the location where your library files are saved. By default, this will be the Documents folder. Relative linking example: If you link a PDF file from your desktop to a record, EndNote will create a copy of that file and store it within the library’s .Data folder. If you remove or rename the original file, the PDF link in EndNote will not be affected.

However, if you turned off “relative” linking, the PDFs will make an “absolute” link to the original file itself. For that reason, the PDFs may be anywhere on your system or network, depending on the original file’s location. Absolute linking example: After changing the default setting in your preferences, if you attach a file that was on your desktop to a record, the link will point to the original file. If you remove or rename the original file, the PDF link in EndNote will no longer function.

3. Why do I only have one file attachments field? How do I attach multiple files?

EndNote stores all attached files in the File Attachments field. You can have Dozens of attachments in a single record. To attach more than one PDF, simply repeat either method of attaching files as many times as needed:

  • Select the record you wish to have the file attached to and choose References>File Attachments>Attach File. Browse to and select the PDF you wish to attach. For relative linking, simply click Open. For absolute linking, uncheck the box at the bottom, labeled “Copy this file to the default file attachment folder and create a relative link,” then click Open. (We recommend using relative links for the best compatibility with online sync and sharing, as absolute links are not shared or synced).
  • Open the record you wish to attach the file to and drag and drop the PDF file onto the record. This will create a relative link to the PDF. (We recommend using relative links for the best compatibility with online sync and sharing, as absolute links are not shared or synced).



1. How do I transfer my Reference Manager Reference IDs into EndNote?

Unlike Reference Manager, the Reference ID numbers in EndNote are not meant to be editable. When you convert your Reference Manager database to EndNote, by default the Reference ID numbers in the Reference Manager database will be copied to the Label field in EndNote, in case you need to refer to these numbers.

2. How do I update my Reference IDs in EndNote?

Unlike Reference Manager, the Reference ID numbers in EndNote are not meant to be editable. When you convert your Reference Manager database to EndNote, by default the Reference ID numbers in the Reference Manager database will be copied to the Label field in EndNote, in case you need to refer to these numbers.
If you have a workflow that requires the use of the Reference ID, it is recommended that you make adjustments to those workflows once you move to EndNote. We do have a method at the bottom of this KB article that allows you to retain the Reference ID numbers when converting to EndNote, but this is only meant for use to convert a document that currently has temporary Reference Manager citations that need to be converted to EndNote, or to address a specific workflow for a one-time conversion to EndNote. Within a given EndNote library on a given computer, the Reference ID numbers will not change. However, the various methods to share that library or move it to a different computer may introduce a complete reordering of the Reference ID numbers, depending on the method used.
When you add a new reference to an EndNote library, that reference is given the next number that has not been used in the library, and deleted references’ numbers are still retained in use in the Library database (so, if you had Reference IDs up to 500 and deleted numbers 495-500, the next new reference would use Reference ID 501, not 495).
Also, when you Sync your library to another computer, or when you copy references from one library to another, those references are given Reference ID numbers sequentially as they are added/imported/Synced, and would not follow the original library’s numbering.

3. How do I enter corporate author names?

Use the steps here:

4. Why aren’t my journal names consistent?

Setup the term list in EndNote using the steps here

5. How do I create synonyms for authors or keywords?

EndNote does not have the same synonym cross-referencing function for author and keyword terms that Reference Manager has. However, you can manually enter additional author and keyword terms in EndNote. To do this, click on the Tools menu, select Open Term Lists and select the Authors or Keywords Term List. Here you can click on New Term to add a term to the appropriate list.

6. How do I copy references between databases/libraries?

There are a few different ways to copy references between EndNote libraries. If you would like to simply merge two existing EndNote libraries, please see this KB article. Alternatively, you can simply copy individual references from one library to another by following this KB article. You can even simply drag and drop references from one open library window to another. All three of these methods would retain any file attachments associated with the references that are copied over.

7. How do I check for duplicates in EndNote?

The steps here:

8. How do I set up an index in my EndNote library?

EndNote does not have the same sort of index that Reference Manager has, but the closest analog would be the Groups function. You can create a Group and add any set of references to it within EndNote. You can also set up Smart Groups, which are essentially saved search results that automatically update when a new reference is added to the library that matches the search criteria. You can even make Combined Groups, which connect Groups and/or Smart Groups together using Boolean terms to include/exclude the sets of other groups.
More information about EndNote’s Groups can be found in this KB article, and in this Training Video.


9. Can I convert my RM custom output styles to use them in EndNote?

No, unfortunately the structure of Reference Manager Styles is different than the EndNote Style file structure. However, we have a much larger selection of precreated EndNote Styles to choose from here on the EndNote website. Also, the editing method between Reference Manager and EndNote is not very dissimilar. You should be able to open up the Style Editing window between both applications side-by-side to make what will essentially be the same Style, if you do not find the file you’re looking for on our website. Additional information can be found in the following EndNote Style Guide, and in this Training Video.

10. How do I use custom reference types in EndNote?

Use the steps here:
Note that custom reference types are stored on the computer as a per user setting unlike Reference Manager. To send another user your custom reference types, use the steps here:

11. Is there a web publisher in EndNote?

No, there is not a function to publish a website containing EndNote references, like the function available in Reference Manager.
If the individuals you are sharing these references with are also using EndNote X7, you can Share your Library with up to 14 other individuals.
Additionally, if you want to share just a portion of your references with a larger group of users, there is the ability to share your EndNote Groups with any number of EndNote online accounts, even the free EndNote Basic version, detailed in this KB article. If you have the ability to host your own Web pages, you can export your library to an html file. This can be done by clicking the File menu and selecting Export. Here you can set the type to “HTML (*.htm).” Keep in mind that we would not be hosting these files.