The objective of the study was to establish the mother–baby pair characteristics that contribute to vertical transmission of HIV and elucidate on remediation. We assessed for factors increasing the odds of HIV transmission in children born to HIV-infected mothers in western Kenya. We used a retrospective study which reviewed routinely collected data of 1 028 mother–baby pairs enrolled in a prevention of mother-to-child transmission (PMTCT) programme in western Kenya from January to December 2015. We compared the transmission rates amongst mothers known to have a positive HIV status before conception (known positives/KPs) versus the transmission amongst those who were newly diagnosed during maternal and child health (MCH) clinic attendance (new positives/NPs). We compared the socio-demographic and clinical characteristics of the mothers using chi square and Kruskal–Wallis tests at 95% confidence interval (CI). We assessed for factors associated with the infants’ HIV status using a logistic regression model. The results revealed that 60% (622) of the mothers were KPs, and that KPs and NPs had mother-to-child transmission (MTCT) rates of 5.5% and 20.7% respectively. Close to 90% of the NP Mothers were at an early HIV clinical stage at enrolment and 40% were enrolled after delivery. The infants of NPs were enrolled at a mean age of 18.3 weeks compared to 6.6 weeks for the infants of the KPs. On adjusted multivariable analysis, child's age at enrolment (AOR = 1.05, 95%CI = 1.036–1.064) and mother's status at conception (AOR = 1.96, 95%CI = 1.042–3.664) were significantly associated with the infant's HIV status. None of the HIV infected infants had received nevirapine prophylaxis. Most of the mothers enrolling into the PMTCT programme have a known HIV-positive status, however, NPs are the largest contributors to continued MTCT.