Background: Human Immunodeficiency Virus (HIV) and thyroid function have been described. Prevalence pattern and atherogenic status significantly differ from HIV-negative control in several studies. Unfortunately, few studies have determined the prevalence of thyroid function and lipids among Nigerians living with HIV. Objective: This study is to evaluate thyroid hormones and lipid profiles in HIV-positive subjects attending a faith-based health facility in Anambra State Nigeria. Materials and methods: The serum concentration of Thyroid Stimulating Hormone (TSH), free Triiodothyronine (fT3), triiodothyronine (T3), free Thyroxine (fT4), Thyroxine (T4), Total Cholesterol [TC], Triglyceride [TG], High-Density Lipoprotein [HDL], Low-Density Lipoprotein [LDL] and Very Low-Density Lipoprotein [VLDL] was determined in 95 HIV positive subjects which include 48 patients who were on HAART- group 1 and 47 not on HAART- group 2; and compared to 30 HIV negative controls – group 3. Results: The level of TSH and fT3 was significantly (p < 0.05) higher in group 1 participants than in group 2 and the group 3 participants. The level of T4 was significantly higher in group 2 than in group 1 and group 3 participants. The level of T3 was significantly lower in Control participants in comparison to both HAART and non-HAART participants. The prevalence of fT4 dysfunction across the groups was significantly different from each other. The total mean of Cholesterol (163.5 ± 22.7), Triglyceride (163.5 ± 22.7), and Very Low-Density Lipoprotein (14.2 ± 2.4) of the HIV-positive participants were significantly (p < 0.05) lower than that of the HIV negative participants. Conclusion: The results obtained from this study indicate that serum levels of thyroid hormones may be used as baseline periodic markers during antiretroviral therapy and many people living with HIV may benefit from supplementation if appropriate.