Introduction The objectives of this study were to investigate the association between HIV infection and dental caries among children in West Africa, and to identify factors associated with dental caries among HIV-infected children. Methods We conducted a multi-center cross-sectional study in Mali, Senegal and Côte d’Ivoire with a random sample of HIV-infected children aged 5-15 years on antiretroviral therapy and their uninfected siblings. A standardized examination was performed by calibrated dentists. The association between the number of decayed, missing or filled permanent and primary teeth surfaces (DMFdefS) and HIV status was investigated by fitting multivariable zero-inflated negative binomial models, for each age group (<12 and ≥12 years). Factors associated with dental caries could be investigated only for HIV-infected children <12 years old. Results The sample included 420 HIV-infected children and 418 non-infected siblings. The median DMFdefS was 7 for the HIV-infected children and 2 for the uninfected siblings. The proportion of children with DMFdefS ≥1 was significantly higher among the HIV-infected children than uninfected children (86.0 percent versus 64.4 percent, P < 0.001). The HIV-infected children were less likely to be caries-free than the uninfected siblings in both age groups. We found a higher degree of caries experience among HIV-infected children < 12 years old, in whom it was associated with sweet drink consumption, history of night bottle use, immunosuppression, and younger age at study entry. Conclusions Although preventable, the burden of dental disease was high in children from families affected by HIV in West Africa and was associated with HIV infection and immunosuppression.