Objective：To study the polymorphism of E6 gene of HPV 52 in Chaozhou. Methods：The DNA was extracted from the cervical exfoliated cells of 101 cases of simple infection of HPV 52. 83 cases of E6 gene complete sequence was amplified success－fully and sequenced. The BLAST 2.0 software online was used for polymorphism study. Results：Totally，76 complete E6 genes were successfully amplified. The similarity was 99% compared with reference strain（GQ472848）. 11 kinds of polymorphism were found，of which 9 kinds were nonsense mutation and the other 2 kinds were sense mutation，which would cause amino acid alteration. All of the 76 cases were divided into Asian cluster and American-European cluster according to the polymorphism of E6 gene. Asian cluster had seven groups. The most common polymorphism was completely matched with the sequence reported in Guangzhou （EU924143） and Hongkong（DQ057293），and this group was named the predominant sequence in Chaozhou area；the variant of the second group was completely matched with the sequence reported in Guangzhou（EU924144）；the variant of the third group was completely matched with the one reported in Zhejiang University reported（HM004117）；while the other 4 groups had never been reported worldwide so far. American-European cluster had three groups. The most common polymorphism was found in 5 different cases，which was com－pletely matched with the sequence reported in America （HQ537745）. The second group polymorphism were found in 2 samples，it was completely matched with sequence reported from America （DQ057291） and Germany （X74481）. The third group was found in one case，which had not been reported before. Conclusion：There is a complicated polymorphism of HPV52 E6 genes in Chaozhou area. The common polymorphism is similar with that reported in the South-east in China or the South-east Asia. The rare sequence matches with American and European reports. This study provides molecular evidence for gene vaccine exploration in Chaozhou.