High risk human papillomavirus (HR-HPV) E2 proteins play roles in transcriptional regulation and arecommonly functionally disrupted when the HPV genome integrates into host chromosomes. Some 15-40%of cancer cases, however, contain an intact E2 gene or episomal HPV. In these cases, polymorphism of the E2gene might be involved. This study aimed to determine polymorphisms of the E2 gene in episomal HPV16detected in high grade squamous intraepithelial lesions and squamous cell carcinomas and altered functionscompared to the E2 prototype. The E2 gene was amplified and sequenced. Two expression vectors containingE2 gene polymorphisms were constructed and transfected in SiHa and C33A cells, then E6 gene as well as Il-10 and TNF-α expression was determined by quantitative RT-PCR. Expression vectors and reporter vectorscontaining the HPV16 long control region (LCR) were co-transfected and transcriptional activity was determined.The results showed that a total of 32 nucleotides and 23 amino acids were changed in all 20 cases of study,found in the transactivation (TA) domain, hinge (H) region and DNA binding (DB) domain with 14, 5 and 13nucleotide positions. They mostly caused amino acid change. The expressing vectors containing different E2gene polymorphisms showed E6 mRNA suppression, TNF-α mRNA suppression and IL-10 induction but nostatistically significant differences when compared to the E2 prototype. Moreover, promoter activity in HPV16LCR was not affected by E2 protein with different gene polymorphisms, in contrast to nucleotide variations inLCR that showed an effect on transcription activity. These results demonstrated that E2 gene polymorphismsof episomal HPV16 did not affect transcriptional regulation and suggested that nucleotide variation as well asepigenetic modification of the LCR might play a role in inducing malignant transformation of cells containingepisomal HPV16.