We have previously shown that O6-methylguanine-DNA methyltransferase (MGMT), a DNA repair protein that protects tissues against toxic and carcinogenic effects of alkylating agents, is degraded through ubiquitination-dependent proteolysis. Here, we investigated the role of the human papillomavirus (HPV) E6 protein in MGMT degradation. In three pairs of isogenic human tumor cell lines in which a member of each pair expressed the E6 protein through stable transfection (HCT116/HCT116-E6, MCF7/MCF7-E6, and RKO/RKO-E6), we found a consistent 40–55% reduction in the MGMT protein level and its activity in all E6-expressing cells compared with the parent cells (P=<0.05). E6 expression did not, however, alter the levels of MGMT mRNA. Addition of the recombinant MGMT (rMGMT) protein to extracts of HCT116/E6 cells resulted in the binding of E6 to MGMT. Further, the purified E6 protein promoted the degradation of rMGMT in rabbit reticulocyte lysates. Immunoprecipitation assays showed the presence of a ternary protein complex between MGMT, E6, and the cellular ubiquitin-ligase E6-associated protein (E6-AP). Transient transfection of the p53-null H1299 lung tumor cells with an E6 construct also down-regulated the MGMT. The MGMT protein also showed structural features that are compatible for interaction with the E6, and E6-AP components. Collectively, these data suggest that the oncogenic E6 proteins enhance the ubiquitin-dependent proteolysis of MGMT.