In a cross-sectional study in 1998 we assessed human immunodeficiency virus (HIV) and syphilis infections and their risk factors among the 316 registered female sex workers (FSWs) of Toliary, south-west Madagascar. No case of HIV infection was detected, but 18.4% of registered FSWs had syphilis. Only half of these women regularly used condoms. In a multiple logistic regression analysis, risk factors for syphilis infection were multiple clients per week and, paradoxically, regular use of condoms. The variables associated with irregular use of condoms were younger ages of registered FSWs, multiple clients per week and Malagasy clients. The high prevalence of syphilis infection associated with irregular use of condoms might facilitate a very fast spread of HIV infection among these FSWs. Promotion of condom use and surveillance of sexually transmitted infections and HIV infection incidence are needed in the south of Madagascar.