Molecular Diversity is a quarterly peer-reviewed scientific journal published by Springer Science+Business Media covering research on molecular diversity and combinatorial chemistry in basic and applied research and drug discovery.

The journal publishes both short and full-length papers, perspectives, news, and reviews.

The journal was established in 1995 and the editors-in-chief are Hong-yu Li and Kunal Roy.

The journal ceased publication at the end of 2000, but was revived when starting in 2003 it absorbed Molecular Diversity Preservation International's Journal of Molecular Diversity (ISSN 1424-7917).

Shu-Kun Lin served as editor-in-chief and edited volumes 6-11 (2003-2007).