Abstract: OBJECTIVE To analyze the relationship between human papilloma virus (HPV) infection and changes of microsatellite (MS) DNA in tissues of Bowen's disease (BD). METHODS The pathological specimens of 30 patients with BD treated in our hospital from Jan. 2011 to Oct. 2015 were selected as observation group, and 30 normal tissue specimens collected at the same period were taken as control group. The types of HPV were detected by gene chip technique, and the relationship between HPV infection and changes of microsatellite DNA in tissues of BD was discussed. RESULTS There were 11 cases of positive HPV infection in observation group, and the infection rate was 36.67%, which was significantly higher than that in control group (P<0.05). In observation group, the subtypes of HPV were all high-risk types, and the proportion of HPV16 subtype infection was the highest (63.64%). The detection rate of MS DNA changes in observation group was 20.00%, which was significantly higher than that in control group (P<0.05), and the proportion of LOH in observation group was higher than that in control group (P<0.05). There were 3 cases of LOH at D17S796 and D17S926 loci associated with tissues of BD and P53, and 1 case of MSI and 2 cases of LOH at D3S1612 and D3S1029 loci associated with mismatch repair gene hMLH1. Among the 11 cases of HPV infection, there were 5 cases of MS DNA changes accounting for 45.45%, among which MSI in MS DNA changes in HPV16 subtype infection accounted for 14.29% and LOH accounted for 42.36%. In HPV58 subtype infection, LOH accounted for 100.00%. There was 1 case of LOH in negative HPV infection, accounting for 5.26%. The incidence of MS DNA changes in HPV positive group was significantly higher than that in HPV negative group (P<0.05). CONCLUSION There are certain correlations between the occurrence of BD and high-risk HPV infection and changes of microsatellite DNA. P53 gene mutation may be involved in the pathogenesis of BD, and there is a certain correlation between high-risk HPV infection and MS DNA changes of BD.