Compugen (Hebrew: קומפיוג'ן‎‎) is a publicly traded drug discovery company headquartered in Israel, with shares traded on the NASDAQ Capital Market and on the Tel Aviv Stock Exchange.

Compugen operates in two areas of the biotechnology industry: it develops and markets bioinformatics software platforms and engages in in silico drug discovery. Over the years it has partnered with companies the likes of Pfizer, Bayer, Novartis, Abbott, BioLineRx, and Seattle Genetics. Roche and Five Prime Therapeutics are among Compugen's competitors.

CGEN-15029 is the lead agent in their immuno-oncology product portfolio.

Compugen was founded in 1993 by Eli Mintz, Simchon Faigler and Amir Natan. Mintz conceived of the idea for the company in 1991 while accompanying his wife, Liat Mintz, to a genomics engagement at the Pasteur Institute in France. She commented that the quantities of data being produced by scientists involved in DNA sequencing exceeded what computers could process at reasonable speeds. Eli Mintz partnered with colleagues Faigler and Natan from the IDF's elite Talpiot program to develop a more powerful computer; and indeed, the company's first computer, dubbed the "Bioccelerator," boasted speeds up to one thousand times faster than other platforms being used at the time. In 1997, the company followed this success by introducing LEADS, an EST clustering and assembly platform. By around 2001, Compugen had effected a shift in its business model from a company whose almost exclusive focus was marketing computer programs and applications to one whose operations extended into the diagnostics and therapeutics fields.

Compugen began trading on the Nasdaq in 2000 and on the Tel Aviv Stock Exchange in 2002. Also in 2002, Compugen spun off its subsidiary Evogene, established as an agriscience division in 1999.

Mor Amitai, Hebrew University alumnus (Ph.D, Mathematics), who joined Compugen in 1994, was the company's CEO and president from 1998 to 2005. He was replaced by Alex Kotzer, Technion alumnus (Chemical Engineering), who was CEO and president through 2008. Anat Cohen-Dayag, Weizmann Institute alumnus (Ph.D, Cellular Biology), became co-CEO of Compugen in 2009, serving alongside Martin Gerstel, Yale alumnus (Engineering). She has been the company's exclusive CEO since 2010.