Reasons for incident cases of vertical HIV transmission in the era of free access to PMTCT in South Africa were investigated. This mixed-methods study was conducted in Soweto, South Africa from June-August, 2009. Birthmothers of HIV-infected infants born after 1 December 2008 were eligible. All participants completed an interviewer-administered questionnaire. Women also participated in a focus group (n = 10) or individual structured interview (n = 35). Mean age of participants (n = 45) was 28.7 years (SD = 5.4). Major findings are: (i) failure of per-guideline prescription of ARV strategies for infants (31%) and/or mothers (57%); (ii) maternal refusal of treatment (n = 5); (iii) preterm delivery (31%); (iv) delayed ANC attendance because of facility-related barriers and maternal apprehension around HIV testing; (v) fear of stigma; (vi) maternal difficulty with administering infant AZT (n = 9) and (vii) maternal confusion about infant feeding. A variety of individual, social, and structural factors must be addressed to optimize PMTCT service delivery in South Africa.