In September 2002, an armed conflict erupted in Côte d'Ivoire which has since divided the country in the government-held south and the remaining territory controlled by the 'Forces Armées des Forces Nouvelles' (FAFN). There is concern that conflict-related population movements, breakdown of health systems and food insecurity could significantly increase the incidence of HIV infections and other sexually-transmitted infections, and hence jeopardize the country's ability to cope with the HIV/AIDS epidemic. Our objective was to assess and quantify the effect this conflict had on human resources and health systems that provide the backbone for prevention, treatment and care associated with HIV/AIDS. We obtained data through a questionnaire survey targeted at key informants in 24 urban settings in central, north and west Côte d'Ivoire and reviewed relevant Ministry of Health (MoH) records. We found significant reductions of health staff in the public and private sector along with a collapse of the health system and other public infrastructures, interruption of condom distribution and lack of antiretrovirals. On the other hand, there was a significant increase of non-governmental organizations (NGOs), some of which claim a partial involvement in the combat with HIV/AIDS. The analysis shows the need that these NGOs, in concert with regional and international organizations and United Nations agencies, carry forward HIV/AIDS prevention and care efforts, which ought to be continued through the post-conflict stage and then expanded to comprehensive preventive care, particularly antiretroviral treatment.