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Autoimmunity plays a role in the development of thyroid dysfunction in human immunodeficiency virus (HIV) infected patients. This study assessed the serum levels of thyroid peroxidise antibody (TPO-Ab) in relation to the various forms of thyroid dysfunction in HIV patients in Kano. Free tri-iodothyronine (fT3), free thyroxine (fT4), thyroid stimulating hormone (TSH) and TPO-Ab were measured using Chemiluminescent immunoassay(CLIA) on the serum of 70 HIV sero-positive patients on Highly Active Antiretroviral Therapy (HAART, as Group I), 70 HAART naïve HIV sero-positive patients (Group II) and 70 apparently healthy HIV negative controls (Group III). The prevalence of thyroid dysfunctions were 55.7%, 42.9% and 2.8% among groups I, II and III respectively. TPO-Ab was elevated in 1 (1.43%) HIV positive patient on HAART, Group I, that also had subclinical hyperthyroidism. Four participants (5.7%) among group III were found to have elevated anti-TPO levels. Thyroid dysfunction was more common among HIV-positive than HIV-negative participants. Thyroid dysfunction among HIV patients was mainly non-autoimmune in origin. However, thyroid autoimmunity appears to play a little role in the development of hyperthyroidism in HIV patients.