The study investigates the risk exposure to HIV infection among South African children aged 2-9 years served by public health services. Together with their biological mothers, 3471 children and were recruited from inpatient and outpatient children in the Free State Province. Blood samples were taken by professional nurses and a history taken of exposure factors associated with HIV transmission. DNA testing was used to confirm biological maternity where the child was HIV-positive and the mother HIV-negative. Mother-child pairs were stratified by mother's HIV status. Exposure factors related to the child's HIV status were examined in each stratum using a chi-square test. Independent factors were then included in a multiple logistic regression model. Having an HIV-positive mother was strongly related to HIV infection in children (OR: 310; 95%CI: 148-781). However, seven HIV-positive children had HIV-negative mothers. Transmission in this group was significantly associated with breastfeeding by a non-biological mother (OR: 437; 95%CI: 53-5020), being fed with expressed breast milk from a milk room (OR: 37.6; 95%CI: 6.2-259.0), dental injection history (OR: 31.5; 95%CI: 4.5-189.4) and visits to a dentist (OR: 26.9; 95%CI: 4.4-283.5). Although mother-to-child-transmission is shown to be the primary mode of HIV transmission in South African children, the few HIV-positive children infected by other modes of transmission suggest a potential risk of non-vertical HIV infections. These infections can be prevented through education and improved infection-control procedures.