Molecules is a peer-reviewed open access scientific journal that focuses on all aspects of chemistry and materials science.

It was established in March 1996 and is published monthly by MDPI.

Molecules was initially published by Springer-Verlag.

In December 1996, Shu-Kun Lin resigned as editor and relaunched the journal with Molecular Diversity Preservation International (MDPI).

Springer initially sued over naming rights, but eventually dropped the suit.