INTRODUCTION:Infection with HIV subtype A has been associated with poorer neurocognitive outcomes compared to HIV subtype D in Ugandan children not eligible for antiretroviral therapy (ART). In this study, we sought to determine whether subtype-specific differences are also observed among children receiving ART. MATERIALS AND METHODS:Children were recruited from a clinical trial in which they were randomized to receive either lopinavir (LPV)- or non-nucleoside reverse transcriptase inhibitor (NNRTI)- based ART (NCT00978068). Age at initiation of ART ranged from six months to six years. HIV subtype was determined by PCR amplification and population sequencing of the pol region derived from peripheral blood mononuclear cell DNA, followed by application of the REGA and Recombinant Identification Programme algorithms. General cognition was assessed using the Kaufman Assessment Battery for Children (Second Edition), attention using the Test of Variables of Attention, and motor skills using the Bruininks-Oseretsky Test of Motor Proficiency (Second Edition). Home environment was assessed using the Home Observation for the Measurement of the Environment (HOME). Age-adjusted test z-scores were entered into a regression model that adjusted for sex, socio-economic status score, HOME score, years of schooling, and ART treatment type. RESULTS:One hundred and five children were tested; median (interquartile range) age was 7.05 years (6.30 to 8.44), CD4 count was 867.7 cells/mm3 (416.0 to 1203.5), and duration on ART was 4.03 years (3.55 to 4.23). Seventy-eight children had HIV subtype A and 27 had subtype D; the groups had comparable home and socio-economic status, except that there were more males among children infected with subtype A than D (64.7% vs. 35.3%, p = 0.02). There were no differences between the subtypes in general cognition (estimated mean difference: 0.20; 95% CI: -0.11 to 0.50); p = 0.21), attention (-0.18, 95% CI: -0.60 to 0.24, p = 0.41) and motor skills (1.60, 95% CI: -0.84 to 4.04, p = 0.20). CONCLUSIONS:Our results imply that ART may diminish the neurocognitive disadvantage seen in treatment-naïve HIV-infected children with subtype A.