We assess the coverage of a Prevention of Mother-to-child Transmission (PMTCT) programme in Busia (Kenya) from 1 January 2006 to 31 December 2008 and estimate the risk of transmission of HIV. We also estimate the odds of HIV transmission according to pharmacological intervention received. Programme coverage was estimated as the proportion of mother-baby pairs receiving any antiretroviral (ARV) regimen among all HIV-positive women attending services. We estimated the mother-to-child transmission (MTCT) rate and their 95% confidence interval (95%CI) using the direct method of calculation (intermediate estimate). A case-control study was established among all children born to HIV-positive mothers with information on outcome (HIV status of the babies) and exposure (data on pharmacological intervention). Cases were all HIV-positive children and controls were the HIV-negative ones. Exposure was defined as: (1) complete protocol: ARV prescribed according World Health Organisation recommendations; (2) partial protocol: does not meet criteria for complete protocol; and (3) no intervention: ARVs were not prescribed to both mother and child. Babies were tested using DNA Polymerase Chain Reaction at six weeks of life and six weeks after breastfeeding ceased. In the study period, 22,566 women accepted testing, 1668 were HIV positive (7.4%; 95%CI 7.05-7.73); 1036 (62%) registered in the programme and 632 were lost. Programme coverage was 40.4% (95%CI 37.9-42.7). Out of the 767 newborns, 28 (3.6%) died, 148 (19.3%) defaulted, 282 (36.7%) were administratively censored and 309 (40.2%) babies completed the follow-up as per protocol; 49 were HIV positive and MTCT risk was 15.86% (95%CI 11.6-20.1). The odds of having an HIV-positive baby was 4.6 times higher among pairs receiving a partial protocol compared to those receiving a complete protocol and 43 times higher among those receiving no intervention. Our data show a good level of enrolment but low global coverage rate. It demonstrates that ARV regimens can be implemented in low resource rural settings with marked decreases of MTCT. Increasing the coverage of PMTCT programmes remains the main challenge.