Most children acquire HIV infection as a result of mother to child transmission (MTCT). The risk of MTCT of HIV is generally estimated at between 15 and 40% without prophylaxis. MTCT was responsible for approximately 370,000 infant HIV infections worldwide with Nigeria accounting for 30%. The study evaluated the effectiveness of prevention of MTCT of HIV infection programme by determining the rate of MTCT of HIV in babies who underwent the programme by review of health records of mother- infant pairs at Olabisi Onabanjo University Teaching Hospital. This was a cross-sectional analytical conducted over twelve years period with medical records of 545 mother-infant pairs analysed. The rate of MTCT of HIV infection was 2.9% compared to 7.1% earlier reported in the centre. The rate of MTCT of HIV was lowest among mother-infant pairs who both received prophylaxis. Ages at recruitment are strong determinant of the risk of infection. Late usage of MTCT prevention service is a risk for HIV infection among exposed infants.