The burden and viral diversity of HIV in Nigeria makes it suitable to evaluate biomedical prevention strategies including HIV vaccines. We document baseline clinical characteristics of a cohort of HIV Exposed Sero-Negative (HESN) partners to highlight background morbidities that might impact the interpretation of research findings especially in low income countries where "normal control" is based on physical appearance and self-reporting. We established a 2-year prospective cohort of HESN, and obtained, at baseline medical history, general physical examination findings and safety laboratory tests results. Among 534 participants with a mean age of 37 ± 9 years, the commonest symptoms were headache (25.5%) and fever (20%), which occurred more among females. Also, 13% reported a history of urethral/vaginal discharge and genital ulcer. High blood pressure (HBP) (i.e. blood pressure ≥ 140/90 mmhg) was a major abnormal examination finding, which occurred more among males (53.2% vs 26.2%, p < 0.01). More female participants had abnormal laboratory results with 31% having low hemoglobin concentration (<12 g/dl, p = 0.021); 30% with elevated alanine transaminase level (p = 0.019) and 28% with abnormal blood urea nitrogen level (p = 0.093). HBP and abnormal safety laboratory are significant findings among so called "normal population" that could affect interpretation of research findings of HIV biomedical prevention studies in Nigeria.