During this first period of laboratory research, he and Pastan and their colleagues described aspects of the mechanism by which the lac operon of E. coli is regulated transcriptionally by cyclic AMP.

During the course of his years at UCSF (1970 to 1993), Varmus's scientific work was focused principally on the mechanisms by which retroviruses replicate, cause cancers in animals, and produce cancer-like changes in cultured cells.

Much of this work and its consequences are described in his Nobel lecture[12] and Bishop's,[13] in Varmus's book The Art and Politics of Science,[10] and in numerous histories of cancer research.

[14][15] Other significant components of Varmus's scientific work over the past four and a half decades include descriptions of the mechanisms by which retroviral DNA is synthesized and integrated into chromosomes;[16][17] discovery of the Proto-oncogene Wnt-1 with Roel Nusse;[18][19] elucidation of aspects of the replication cycle of hepatitis B virus (with Donald Ganem[20]); discovery of ribosomal frameshifting to make retroviral proteins (with Tyler Jacks[21]); isolation of a cellular receptor for avian retroviruses (with John Young and Paul Bates[22]); characterization of mutations of the epidermal growth factor receptor gene in human lung cancers, including a common mutation that confers drug resistance (with William Pao[23]); and generation of numerous mouse models of human cancer.

[25] After the resignation of NIH Director Bernadine Healy in April, 1993, Varmus was nominated for the post by President William J. Clinton in July, and confirmed by the Senate in November.

[28] Varmus declared his support for Barack Obama's quest for the presidency early in 2008[29] and chaired the campaign's Science and Technology Committee.

In this capacity, despite diminishing budgets at all the Institutes including NCI, he started new administrative centers for cancer genomics and global health; initiated novel grant programs for "outstanding investigators," for "staff scientists," and for addressing "Provocative Questions.

During his tenure as NCI Director, Varmus took the unusual step of co-authoring with three non-governmental colleagues a critique of several practices prevalent in the biomedical research community.

[38] After leaving the NIH Directorship at the end of 1999, Varmus became the president and CEO of Memorial Sloan-Kettering Cancer Center in New York City on January 1, 2000.

During his ten and a half years at MSKCC, he was best known for enlarging the basic and translational research faculty; building a major new laboratory facility, the Mortimer E. Zuckerman Research Center; starting a new graduate school for cancer biology (the Louis V. Gerstner Jr. Graduate School of Biomedical Sciences); overseeing renovation and construction of many clinical facilities; and leading a major capital campaign.

He has been chair of the World Health Organization's Science Council since its founding in 2021[49] Varmus has criticized the high cost of many modern cancer drugs, which create barriers to treatment.

He argues that widespread use of panel tests and exome analyses to identify cancer-causing mutations would be simpler and cheaper than full genome analysis.