Objective To estimate the female sex worker population size in three cities in Coˆ te d’Ivoire and in Kisumu, Kenya. Methods Capture–recapture was used, calculating size estimates by first ‘tagging’ a number of individuals and, through an independent recapture, calculating the proportion of overlap. The same procedures were used in all four cities. In the first phase, members of the target population were ‘captured’ and ‘marked’ by giving them a capture card. Six days later, in the same places and at the same time, a second sample was ‘captured’, which comprised a certain number of people who were captured in the first round. During the exercise, questions were asked to estimate the coverage of the sex worker clinics. results Using capture–recapture, the estimated number of female sex workers was 1160 in Yamoussoukro (95% CI 1053–1287), 1202 in Bouake´ (95% CI 1128–1279), 1916 in San Pedro (95% CI 1809–2030) and 1350 in Kisumu (95% CI 1261–1443). The proportion of female sex workers in Coˆ te d’Ivoire who had visited the clinic ranged from 15% in Yamoussoukro to 30% in San Pedro and was 34% in Kisumu. Conclusions Capture–recapture was successfully applied to estimate the population size of female sex workers. These estimations were urgently needed to help mobilize an increased response to HIV, to assess programme coverage and to estimate potential impact of the targeted intervention.