Sequence variations within the genome of human papillomavirus (HPV) type 16 have been reported in different ethnic populations, with some evidence suggesting that non-European variants may confer higher oncogenic potential. HPV16 European (EUR) and Asian (As) variants were identified previously as two major variants in cervical cancer from Anyang, China. The evolutionary analysis of these variants revealed that several important sequence variations in the E6 and E2 genes were under positive selection pressure. The aim of this study was to evaluate the effects of these variations on E6 and E2 functions regarding p53 degradation and transcription regulation of the long control region (LCR). By Western blot analysis, a similar ability to degrade p53 was observed among EUR E6, As E6, EUR E6-L83V and As E6-E113D. A rare variation, EUR E6-R10G, was found to shorten the half-life of p53 more efficiently than the other variations. Unlike EUR E2 acting as a transcriptional activator or a repressor at different concentrations, As E2 showed a dose-dependent repression of LCR activity, about twofold stronger than EUR E2 in the luciferase reporter assays. Furthermore, the site-directed mutagenesis revealed that E232K, which is a linked variation in the hinge region of As E2, was responsible for its enhanced repression ability. Collectively, these data indicate the altered functions of HPV16 E6 and E2 by certain variations, which may influence the potential of viral carcinogenesis. J. Med. Virol. 86:618–626, 2014. © 2013 Wiley Periodicals, Inc.