The software's primary function is to organize references and maintain a digital library of PDF documents.

Papers was developed by Alexander Griekspoor and Tom Groothuis while studying towards their PhD diplomas at the Netherlands Cancer Institute.

[1] The pair worked on Papers to provide an approach to document management that was similar to the iTunes application on macOS, after they were faced with hundreds of digital publications in PDF format.

Both products received a considerable amount of criticism from users, who experienced a number of issues, ranging from lost databases and annotations to incompatibility between mobile and desktop apps.

It also allows users to access their library and insert citations across a variety of different applications, whether in documents, presentations, or in web browsers.

This version introduces a redesigned user interface and Dropbox based syncing, which has subsequently been expanded to other cloud-based repositories.

A new version, now Papers 3 for Windows, was released late July 2014 following the redesign of the Mac and iOS applications earlier.

Papers won an Apple Design Award in 2007, for best Mac OS X Scientific Computing Solution.