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Background  Publications on Libya’s HIV epidemic mostly examined the victims of the tragic nosocomial HIV outbreak in the 1990s and the related dispute about the detention of foreign medical workers. The dispute resolution in 2003 included an agreement with the European Union on humanitarian cooperation and the development of Libya’s first National HIV Strategy. As part of this we conducted Libya’s first bio-behavioural survey among men having sex with men (MSM) and female sex workers (FSW).    Methods  Using respondent-driven sampling, we conducted a cross-sectional study to estimate the prevalence of HIV, hepatitis B virus (HBV), hepatitis C virus (HCV), and related risk factors among 227 MSM and 69 FSW in Tripoli (FSW recruitment ended prematurely due to the political events in 2011).    Results  For MSM we estimated an HIV prevalence of 3.1%, HBV prevalence of 2.9%, and HCV prevalence of 7.3%, and for FSW an HIV prevalence of 15.7%, HBV prevalence of 0%, and HCV prevalence of 5.2%. We detected high levels of risk behaviours, poor HIV-related knowledge, high stigma and lack of prevention programmes. These results must be interpreted in the context of the political situation which prohibited reaching an ideal sample size for FSW.    Conclusion  There is urgent need to implement an effective National HIV Strategy informed by the results of this research. The risk of transmission within different risk groups and to the general population may be high given the recent military events that led to increased violence, migration, and the disruption of essential HIV-related services.

Filling the Knowledge Gap: Measuring HIV Prevalence and Risk Factors among Men Who Have Sex with Men and Female Sex Workers in Tripoli, Libya