Background: The quality of life and life expectancy of individuals living with HIV has improved significantly. This improvement is largely due to the use of Highly Active Anti-Retroviral Therapy (HAART). The effect of prolonged usage of this therapy on the menstrual function of the females within the reproductive age range is poorly understood. Methodology: A cross-sectional comparative study that involved women within the reproductive age range of 15-45 years. The women were grouped into A, B and C categories. Group A had HIV positive women already on Anti-Retroviral (ARV) therapy. Group B were HIV positive women naïve to anti-retroviral drugs at the time of recruitment. Group C comprised of HIV negative women within the reproductive age range not being managed for infertility. Results: The mean age of the participants across the study groups were respectively 32 years, 33.4 years and 37.58 years. The average weight among participants in the study was 66.38 kg, with a range of 53- 94 kg. The average duration of use of ARVs was 81.12 months (6.7 years). The mean CD4 values across the study population who were HIV positive were 725 and the average viral load was 20 copies per ml. The commonest menstrual abnormality was oligomenorrhea, occurring in close to 25% of respondent who were HIV positive and on ARVs. Menstrual abnormality was more in the HIV positive women receiving antiretroviral drugs than in the other two cohorts. (p=0.007). Conclusion: Long term usage of some first line highly active anti-retroviral therapy is associated with increased menstrual abnormality.