Background: The study was undertaken to explore and generate information on the morbidity patterns in HAART Naïve HIV infected adults on oral Cotrimoxazole prophylaxis (CTXp) attending Mbagathi and Kenyatta National Hospitals, comprehensive care centres.Methods: A qualitative , retrospective study design of mixed methods was used which comprised; Clinical data extraction and Secondary data analysis of 450 personal medical records that existed and which met inclusion criteria based on age, baseline CD4+ cells ≥ 350 count, non-pregnant, absence of active TB and on CTXp for duration of six months at the time of enrollment.Results: The study showed that patients in both Mbagathi district and Kenyatta National hospitals comprehensive care centres (CCC) had at baseline CD4+ cells range; 350-600 and later at 12 months CD4+ cells range; 400-1500. Patients of younger age, when given CTXp, had a consistent high CD4+ cells count (above 1000 CD4+ cells count) while those of older age had CD4+ levels that were fluctuating. The median age was 31 years. In over 50% documentation, common infections were frequent and patients treated with essential antimicrobial drugs. We observed that CTXp prophylaxis may have reduced severity of infections and this could also have supported up to 60% of the resolved infections. The self-reported adherence to CTXp was observed as part of quality monitored care.Conclusion: The findings of this study support work in a number of literature in other studies done outside Kenya on CTXp not associated with a worsened progression of HIV disease. Stockouts should be avoided due to public health implications. Further studies may be done to find out what potential CTXp has on HIV infected Kenyan patients with serious threat of bacterial infections in conjunction with the customized highly active antiretroviral therapy (HAART)
