A prospective cohort study on the mother-to-child transmission of human immunodeficiency virus type 1 (HIV1), type 2 (HIV2) and dual positivity (HIV1 + HIV2) was carried out in Banfora, West Burkina Faso. The study samples consist of 117 newborns of HIV-seropositive women matched to 234 newborns of HIV-seronegative women. Among cases, 91 were born of HIV1-seropositive mothers, 15 were born of HIV2-seropositive mothers and 11 were born of HIV1 and HIV2 dual-seropositive mothers and were included in an 18-month follow-up. Calculation of the mother-to-child transmission rate was according to the recommendations of the European Economic Community working group. The HIV1 mother-to-child transmission rate was estimated to be 27.8% (95% confidence interval (CI) 24.5 to 32.4) with one method and 25.5% (95% CI 13.5 to 37.5) with a second method. For HIV2, this rate was estimated to be 29.5% (95% CI 26.0 to 39.8) and was not statistically different from the HIV1 mother-to-child transmission rate. No case of transmission was observed in children born of dual seropositive mothers. Survival rate at month 18 was significantly lower for children born of HIV1 mothers: 83.7% (95% CI 78.2 to 92.2). Survival rates were similar between children born of HIV2-seropositive (86.7), dual HIV1 + 2-positive (100) and seronegative mothers (92.0%). Findings suggest a higher mother-to-child transmission rate of HIV2 in children born in Burkina Faso than in Europe and a low clinical expression of HIV2 in children.