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Objective: To evaluate the impact of ART of the mother and the child on the HIV status of children born to HIV positive mothers in compliance with the policy of mother-child transmission (PMTCT) adopted in Burkina Faso. Method: It is a prospective cohort study. 214 HIV-positive mother - infant pairs were involved over a period of 14 months (2011-2013). Early pediatric laboratory biologic diagnosis of HIV infection with children aged from 6 weeks to 18 months was carried out by RNA/PCR of HIV1 (Kit Biocentric®). Children with viral load lower than 300 copies/mL (>2.48 Log) were considered uncontaminated. All the children were clinically and biologically followed up to 18 months, the age at which an immunochromatographic test (Determine®) and an ELISA test (Immunocoomb II BiSpot HIV1 2®) were made to confirm their serological status. We determined the immunological status of positive mothers through a numeration of TCD4 + lymphocytes on a flow cytometer (FacscountV1.5). HIV positive Women were dispatched following treatment systems in accordance with options A and B + (mothers on nevirapine alone, mothers on highly active antiretroviral therapy (HAART)/mothers without HAART). Results: The median age of the children was 6 months (1.5-18 months). The sex ratio was 0.79. The infection rate was 11.2% (24/214). The MTCT was significantly higher among mothers without HAART on Nevirapine only (22/41) than among those on HAART (2/172) p=0.0000 2. The proportion of children infected through breastfeeding whose mothers were not on HAART (23/23) was significantly higher than those whose mothers were on HAART (0/139) p=0.0000 12. Conclusion: According to the guidelines combined on the use of antiretroviral for the treatment and prevention of HIV infection (June 2013), we also recommend for Burkina Faso, the abandonment of Option A and the adoption of option B + with all pregnant women whatever their immune-clinical status.