Background: Mother to child HIV transmission is a significant public health problem especially in Southern Africa. South Africa is the second highest burden country globally with 71 000 infants being HIV infected every year. The aim of this study was to identify and measure the influence of risk factors of late postnatal HIV transmission and/or mortality among infants born to HIV positive mothers. Study design: Historical cohort data collected during 2002 - 2004 from 3 purposively selected PMTCT sites in South Africa (namely: Rietvlei, Umlzai and Paarl) is used. These three sites are purposively selected to reflect different HIV prevalence, socioeconomic and geographical locations. A total sample size of 469 mother-infant pairs were followed for 36 weeks. Data Collection: Data were collected by trained field researchers and community health workers using semi-structured interviews including: infant feeding practices, infant and maternal mortality, disclosure of HIV status, basic knowledge of HIV/AIDS and MTCT and sociodemographic information.