Kidney disease occurs frequently among HIV infected individuals and is becoming a leading contributor to morbidity and mortality in patients with HIV. Early detection of kidney damage using a simple and relatively inexpensive procedure will aid in instituting interventional measures that could slow down or halt the progression of kidney disease. This study was undertaken to determine the prevalence and risk factors for microalbuminuria in HIV infected children in Jos, Nigeria. The Subjects and Controls consisted of 135 age and sex matched HIV infected and uninfected children from one to eighteen years of age. HIV infected children were recruited from the Paediatric AIDS Prevention Initiative in Nigeria (APIN) clinic while uninfected children were recruited from the Paediatric Outpatient Clinic, both units of the Jos University Teaching Hospital. Participants with overt proteinuria and those at risk of microalbuminuria were excluded. Spot urine and blood samples were obtained from Subjects and Controls and were analyzed for microalbuminuria and serum creatinine. Student’s t test was used for comparison of means while categorical variables were compared using chi square test and Fisher’s exact test as appropriate. Multiple logistic regression analysis was used for determination of the association between the prevalence of microalbuminuria and various predicted risk factors. P values < 0.05 were taken as significant. Thirty (22.2%) Subjects and 13 (9.6%) Controls (p = 0.001) had microalbuminuria. There was no significant difference between mean ages of Subjects with versus without microalbuminuria (11.0 ± 3.1 years versus 10.58 ± 4.6 years; p = 0.57). There was also no significant difference between the prevalence of microalbuminuria in males versus female Subjects (27.0% versus 18.1%, p = 0.21) and between male and female Controls (9.5% versus 9.7%, p = 0.92). Furthermore, there was also no significant difference between the mean time since HIV diagnosis among Subjects with microalbuminuria 8.6 ± 3.9 years and those without (7.7 ± 3.4 years; p = 0.22). Majority of the Subjects (97%) were on HAART. Forty eight percent of Subjects in WHO clinical stage II versus 16.4% of those in clinical stage I had microalbuminuria (p = 0.01). It is concluded that the prevalence of microalbuminuria is high in both HIV infected and uninfected children. It is also concluded that the prevalence is significantly higher among HIV infected children and that an increasing WHO clinical stage is a significant risk factor for the development of microalbuminuria. It is recommended that both HIV infected and uninfected children should be screened for microalbuminuria as part of the school health program.