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Within an ongoing HIV/STD prevention project aimed at female sex workers (FSW) in Cotonou, Benin, we evaluated time trends in HIV and STD prevalences from 1993 to 1999.Three serial cross-sectional surveys were conducted in 1993 (n = 374), 1995–1996 (n = 365), and 1998–1999 (n = 591). A questionnaire was administered to the FSW and they were screened for HIV, syphilis, Neisseria gonorrhoeae, and Chlamydia trachomatis.The mean percentage of condom use with clients in the week preceding the interview increased from 62.2% in 1993 to 80.7% in 1998–1999 (P = 0.0001). The prevalence of all infections decreased significantly (all P < 0.02; chi-square for trend) over time: HIV from 53.3% in 1993 to 40.6% in 1998–1999; syphilis from 8.9 to 1.5%; gonorrhoea from 43.2 to 20.5%; and chlamydia from 9.4 to 5.1%. However, the mean age of FSW decreased from 31.0 to 28.4 years between 1993 and 1998–1999. Moreover, the country of origin of these women changed dramatically over time: the proportion of Ghanaian women decreased from 66.3% in 1993 to 21.6% in 1998–1999 when the predominant group became Nigerian (38.0%). When controlling for age and country of origin, HIV prevalence was stable over time (P = 0.71), whereas the downward trend remained significant for syphilis and gonorrhoea (both P < 0.001), and was present but not significant for chlamydia (P = 0.13).These data suggest that the time trends in HIV and STD prevalences are partly due to the changing sex work milieu, but that the intervention also had an impact. Prevention programmes aimed at FSW should be highly prioritized.