Objective: To study the genetic variation characteristics of HPV56 E6, E7 and L1 in patients with precancerous lesions infected with HPV56, and to obtain the molecular epidemiological data of HPV56 in patients with precancerous lesions of cervical cancer in Yunnan. Methods: A total of 300 cervical intraepithelial neoplasia patients were enrolled and HPV genotyping kit was used to detect the types of HPV infection in the patients. The HPV E6, E7, and L1 genes in patients infected with HPV 56 were sequenced. Finally, the lineage distribution of HPV 56 and the genetic variations of HPV 56 E6, E7, and L1 genes in the study subjects were analyzed. Results: In this study, the HPV56 virus infected by the study subjects mainly belonged to the A lineage, with more than 90% belonged to the A lineage, and about 10% belonged to the B lineage. There were 13 mutation loci in the E6, E7 and L1 genes of HPV56, including 6 in the E6 gene, 4 in the E7 gene and 3 in the L1 gene. Among the 6 mutation sites of HPV56 E6 gene, 2 were synonymous mutations (T158C (S19S), G437A (P112P)), and 4 were non-synonymous mutations (A141C (S14R), A241G (N47S), A263C (K54N), G279A (D60N)). The four mutation sites of HPV56 E7 gene were all non-synonymous mutations (C601A (D10E), G605A (V12I), G770C (E67Q), G802C (Q77H)). Among the three mutation sites of HPV56 L1 gene, two were synonymous mutations (G6454T (P321P), A6868C (I459I)), and one was non-synonymous mutation (A5867G (N126D)). Conclusion: This study obtained preliminary data on the genetic variations of HPV 56 E6, E7, and L1 genes in CIN patients in Yunnan area, and obtained the molecular epidemiological characteristics of HPV 56 E6, E7, and L1 genes. It provides necessary data for further analysis of the molecular epidemiological characteristics of HPV 56 E6, E7, and L1 genes in CIN patients in Yunnan area. [ABSTRACT FROM AUTHOR]