The objectives of this study were to estimate the prevalence of Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) infection among female sex workers (FSWs) in an HIV/AIDS high-risk area in China and to examine risk factors associated with CT or NG infection. A cross-sectional study of 568 FSWs was conducted in Kaiyuan City, Yunnan Province, PR China. The prevalence rates of HIV, CT and NG in the study participants were 11.1%, 17.4% and 8.3%, respectively. More than one-fifth (21.3%) of participants tested positive for either CT or NG. This study identifies a relatively high prevalence of CT or NG infection among FSWs in Kaiyuan. Notably, HIV infection was found to be associated with NG infection and study participants who tested positive for NG had a higher rate of CT infection. Further studies are warranted to examine the prevalence and spread of CT and NG in China, and their potential impact on the HIV epidemic.