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There is evidence that children who are HIV positive (HIV +) are at risk for poor developmental outcomes. The aims of this study were to use developmental screening tools to measure outcomes of children affected by HIV/AIDS attending community-based organisations (CBO) and to determine what types of CBO provision these children were receiving. In a cross-sectional study, we interviewed 979 children and their carers (4 to 13 years) at 28 randomly selected CBOs funded by 11 major donors in South Africa and Malawi. Developmental outcomes were assessed using the Ten Questions childhood disability screening tool and the Strengths and Difficulties Questionnaire. Health-related quality of life was measured using the Paediatric Quality of Life Scale. Overall, 13.8% (n = 135) were HIV +. HIV + children were more likely to have developmental difficulties and lower health and educational quality of life, controlling for a range of factors. Developmental difficulties and poorer quality of life were predicted by being HIV +, living in South Africa, not attending school regularly, poor housing conditions and living with a sick family member. HIV + children tended to have been enrolled in CBO programmes for a longer period compared to other children but reported lower rates of contact. A greater proportion of HIV + children received medical services, psychosocial interventions and emotional support, compared to HIV − children. However, fewer HIV + children were enrolled in play groups, early childhood intervention programmes and educational programmes. Screening for developmental problems using short tools is possible in community settings in order to identify children with developmental difficulties and plan services for children infected with and affected by HIV. This study highlights the important role of CBOs to intervene to improve child development outcomes. The delivery of evidence-based services that target child development outcomes will enable HIV-infected children to meet their developmental potential and promote their participation in their communities.