The aim of this study was to assess antenatal transmission of hepatitis B virus in a context of moderate prevalence of HIV in Burkina Faso. Among 360 counselled pregnant women for HIV and HBV testing, 307 were voluntarily enrolled at their last antenatal clinic at the university hospital, in Ouagadougou. Blood samples were collected from all the 307 mothers and tested for HBsAg, HBeAg and antibodies to HIV Blood samples were collected from 313 newborns in the 24 hours after birth and screened for HBV Data from mothers and newborns were collected and analysed using the EPI Info 2002 software. Values for p < 0.05 were considered statistically significant. HBsAg were found in 35 (11.4%) mothers, including 7 with HBeAg and 6 co-infected by both HIV and HBV. Seven babies born to 13 carrier mothers for HBsAg and HBeAg had HBsAg versus 6 born to 22 HBsAg carrier mothers HBeAg-negative. HBsAg was detected in 4 babies born to 6 HIV/HBV co-infected mothers versus 9 born to 29 mothers with HBsAg and HIV-negative. HIV infection, HBeAg and mothers excision were significantly associated with mother-to-child transmission (MTCT) of HBV (p < 0.02). HBV antenatal transmission was important in Ouagadougou and it occurred 2.5 folds more from HIV coinfected mothers than in HIV-negative mothers to newborns. These results showed the need of the implementation of national programme for HBV screening and immunisation in Burkina Faso.