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To determine the probable route of transmission of HIV to children aged 12 years or younger in a rural area of Uganda from 1999 through 2000 and to examine associations between HIV infection and health care-related variables.The HIV infections status for 6991 children was determined from 1 round of an ongoing population surveillance system, and the reported numbers of injections in the past year and blood transfusions were determined for 5922 of these children based on a medical questionnaire. Data from the surveillance system and from an additional survey were used to assess the potential for vertical infection from a mother to her child.The HIV prevalence among children was 0.4%. Of 23 definite and 4 probable cases of HIV infection in children, vertical transmission was not possible for 1 case, not likely for another case, and possibly not vertical for another case. The population-attributable fraction for vertical transmission was between 90% and 94%. Large numbers of injections in the past year and ever having a blood transfusion were only associated with HIV infection in children exposed to vertical transmission.Up to 10% of HIV infections in children in the study area were not attributable to vertical transmission, and thus were possibly attributable to iatrogenic transmission. Associations seen between health care-related variables and HIV were likely to be attributable to treatment for AIDS-related illness in children infected vertically.