BACKGROUND: In eastern and southern Africa, the human immunodeficiency virus (HIV) epidemic appeared first in urban centres and then spread to rural areas. Its overall prevalence is lower in West Africa, with the highest levels still found in cities. Rural areas are also threatened, however, because of the population's high mobility. We conducted a study in three different communities with contrasting infection levels to understand the epidemiology of HIV infection in rural West Africa. METHOD: A comparative cross-sectional study using a standardized questionnaire and biological tests was conducted among samples in two rural communities of Senegal (Niakhar and Bandafassi, 866 and 952 adults, respectively) and a rural community of Guinea-Bissau (Caio, 1416 adults). We compared the distribution of population characteristics and analysed risk factors for HIV infection in Caio at the individual level. RESULTS: The level of HIV infection was very low in Niakhar (0.3%) and Bandafassi (0.0%), but 10.5% of the adults in Caio were infected, mostly with HIV type 2 (HIV-2). Mobility was very prevalent in all sites. Short-term mobility was found to be a risk factor for HIV infection among men in Caio (adjusted odds ratio (aOR) = 2.06; 95% CI: 1.06-3.99). Women from Caio who reported casual sex in a city during the past 12 months were much more likely to be infected with HIV (aOR = 5.61 95% CI: 1.56-20.15). Short-term mobility was associated with risk behaviours at all sites. CONCLUSIONS: Mobility appears to be a key factor for HIV spread in rural areas of West Africa, because population movement enables the virus to disseminate and also because of the particularly risky behaviours of those who are mobile. More prevention efforts should be directed at migrants from rural areas who travel to cities with substantial levels of HIV infection.