The aim of this study was to identify factors associated with prevention of mother-to-child transmission (PMTCT) in an area of Kenya with widely accessible free PMTCT services. A matched case-control study was conducted at 31 public facilities in western Kenya. HIV-infected mothers with infants aged 6 weeks to 6 months were interviewed and medical charts were reviewed. Cases were mothers of infants with a definitive diagnosis of HIV. Controls were mothers of infants testing HIV negative. Cases and controls were matched in a 1:3 ratio on socio-demographic factors. Fifty cases and 135 controls were enrolled. Conditional (matched) logistic regression analysis was conducted. Odds of being a case were higher for women who first learned their HIV status during pregnancy [OR:2.85, 95%CI:1.41–5.78], did not adhere to antiretroviral therapy (ART) [OR:3.35, 95%CI:1.48–7.58], or had a home delivery [OR:2.42, 95%CI:1.01–5.80]. Based on medical record review, cases had higher odds of their provider not following guidelines for prescription of ART for mothers [OR:8.61, 95%CI:2.83–26.15] and infants [OR:9.72, 95%CI:2.75–34.37]. Stigma from the community [OR:0.37, 95% CI:0.14–1.02] or facility [OR:0.38, 95%CI:0.04–3.41], did not increase the odds of MTCT. Poor adherence to PMTCT guidelines and recommendations by both infected women and health care providers hamper efforts to attain elimination of MTCT.