BACKGROUND: Provider-initiated HIV testing and counseling (PITC) is offered as part of the normal standard of care to increase access to treatment for HIV-infected children. In practice, HIV diagnosis occurs in late childhood following recurrent and chronic infections. We investigated primary caregivers' reported reasons for seeking HIV testing for children aged 5-18 years, determined the orphan status of the children, and compared the clinical profile and disease burden of orphans and non-orphans. METHODS: This was a cross-sectional survey of primary caregivers of HIV-infected children accessing antiretroviral treatment (ART) from two community hospitals and 34 primary healthcare facilities in a rural district in Mpumalanga province, South Africa. RESULTS: The sample consisted of 406 primary caregivers: 319 (78.6%) brought the child to the health facility for HIV testing because of chronic and recurrent infections. Almost half (n = 183, 45.1%) of the children were maternal orphans, 128 (31.5%) were paternal orphans, and 73 (39.9%) were double orphans. A univariate analysis showed that maternal orphans were significantly more likely to be older (OR = 2.57, p = 0.000, CI: 1.71-3.84), diagnosed late (OR = 2.48, p = 0.009, CI: 1.26-4.88), and to start ART later (OR = 2.5, p = 0.007, CI: 1.28-4.89) than non-orphans. There was a high burden of infection among the children prior to HIV diagnosis; 274 (69.4%) presented with multiple infections. Multiple logistic regression showed that ART start age (aOR = 1.19, p = 0.000, CI: 1.10-1.29) and time on ART (aOR = 2.30, p = 0.000, CI: 1.45-3.64) were significantly associated with orphanhood status. Half (n = 203, (50.2%) of the children were admitted to hospital prior to start of ART, and hospitalization was associated with multiple infections (OR = 1.27, p = 0.004, CI: 1.07-1.51). CONCLUSIONS: The study found late presentation with undiagnosed perinatal HIV infection and high prevalence of orphanhood among the children. The health of maternal orphans was more compromised than non-orphans. Routine PICT should be strengthened to increase community awareness about undiagnosed HIV among older children and to encourage primary caregivers to accept HIV testing for children.