The incidence/mortality rates of esophageal squamous cell carcinoma (ESCC) vary widely in different parts of China. Human papillomavirus (HPV) infection is considered a possible risk factor. Loss of heterozygosity (LOH) analysis on 87 ESCC specimens collected from three different areas of China showed lower frequency of LOH at marker D3S1621 in Linxian, an area with exceptionally high incidence of ESCC but low HPV infection rate. HPV-positive ESCC from Hong Kong, but not Sichuan, had higher frequency of LOH at D5S82 (APC, MCC), D6S497 (p21/Waf-1, HLA) and D13S260 (BRCA2) than HPV-negative samples. Our results suggest that different genetic pathways of carcinogenesis may be associated with geographic differences in risk factors.