To evaluate HIV/STI prevalence among female sex workers (FSWs) in Botswana, and assess HIV-related risk behaviors. Cross-sectional study using time-location sampling in three districts of Botswana. Adjusted HIV prevalence at district level ranged from 53.5 to 68.5 %. Syphilis prevalence ranged from 3.7 to 14.5 %; chlamydia prevalence ranged from 4.8 to 16.3 %; and gonorrhoea prevalence ranged from 8.3 to 11.7 %. FSWs had been practicing sex work for a mean of 4.7 years, and had a mean of 7.6 sex partners in the week before the survey. While 67.1 % of FSWs surveyed reported always using condoms with clients in the past month. 59.5 % reported one or more of the following: being paid more not to use a condom, having a condom break, or being forced not to use a condom by clients. Predictors of HIV infection in the multivariate analysis included: age (over 30 years), perceiving oneself to be at high risk of HIV, selling sex for 2 or more years, and having a mean of 11 or more partners in the last week. High HIV prevalence, high rates of partner exchange, a sizable population, and Inconsistent condom use combine together help fuel the country’s hyper epidemic. HIV prevention interventions need to take into account the important influence of clients and boyfriends on condom use behavior.