Thyroid disorders have been described in an adult population but are underreported in the pediatric population. The aim of this study was to determine the prevalence and describe the spectrum of thyroid abnormalities among HIV infected children on Highly Active Antiretroviral Therapy (HAART) in Lagos, Nigeria. This was a cross-sectional study carried out at a teaching hospital with an antiretroviral therapy (ART) center. Serum levels of thyroid stimulating hormone (TSH), free triiodothyronine (fT3), and free thyroxine (fT4) were analyzed in 83 children living with HIV on HAART and 51 controls. The prevalence of thyroid dysfunction and correlation of fT3, fT4, and TSH with duration on HAART, age, CD4 count, and nutritional status were assessed. Thyroid abnormalities were seen in 9.6% of the children living with HIV comprising subclinical hypothyroidism in 6%, euthyroid sick syndrome in 2.4%, and overt hypothyroidism in 1.2% as compared to 2% subclinical thyroid disease among the controls (p= 0.15). Hypothyroidism was correlated with CD4 count and viral load. None of the patients had clinical features of thyroid disease. Thyroid abnormalities were more prevalent among children living with HIV and yearly screening with follow-up is advocated.