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Capture-recapture methodology has been employed to estimate the size of hidden or difficult-to-reach human populations such as sex workers, homeless persons, and intravenous drug users. This study took place in the context of efforts to improve the quality of curative and preventive services for sexually transmitted infections offered to sex workers in Diego-Suarez, Madagascar in partnership with sex workers.The goal of this study was to better understand sex-trading practices, map out sex work sites, and estimate the size of a mobile sex-worker population in Diego-Suarez, Madagascar using methods that can be reproduced in other resource-poor settings.Forty sex workers were trained to function as field researchers. Key informants in designated neighborhoods were identified and interviewed. Basic maps of sex-trade sites were designed by hand. The number of sex workers in Diego-Suarez was estimated using capture–recapture methodology. An educational brochure was used to “capture” sex workers during a first phase, and “recapture” 2 weeks later.Most sex trade was street based and mobile. Capture–recapture methods estimated a total of 2684 sex workers (95% CI: 2588–2780) in Diego-Suarez, or approximately 12% of the 15- to 49-year-old female population in the city.Geographic mapping and capture–recapture proved to be low-cost and relatively easy to use techniques for counting a hard-to-reach population, such as female street-based sex workers. Sex workers can be capable fieldworkers, and their active participation in research concerning sex work should be considered whenever possible. A high proportion of women of reproductive age were found to engage in sex work, indicating that there is an urgent need to scale up sexually transmitted infection and HIV prevention activities targeting sex workers, their sexual partners, and the general population.