BackgroundWe conducted a study to assess the frequency and distribution patterns of selected opportunistic infections (OIs) and opportunistic cancers (OCs) in different geographical areas before and after HAART in Uganda.MethodsThis was a cross-sectional serial review of observation data for adult HIV positive patients (≥15 years) enrolled with the AIDS support organization (TASO) in Uganda covering the period from January 2001 to December 2013. Both AIDS defining OIs/OCs and non-AIDS defining OIs were analyzed. The study period was structured into three time periods: “pre- HAART” (2001–2003), “early-HAART” (2004–2008) and “late-HAART” (2009–2013). Descriptive statistics were used to summarize the data by time period, age, gender and geographical location. Chi squared test used to test the significance of the differences in proportions.ResultsA total of 108,619 HIV positive patients were included in the analysis. 64% (64,240) were female with median age of 33 years (IQR 27–40). The most frequent OIs before HAART were oral candida (34.6%) diarrhoeal infection (<1 month) (30.6%), geohelminths (26.5%), Mycobacterium tuberculosis (TB) (17.7%), malaria (15.1%) and bacterial pneumonia (11.2%). In early HAART (2004–2008), the most frequent OIs were geohelminths (32.4%), diarrhoeal infection (25.6%), TB (18.2%) and oral candida (18.1%). In late HAART (2009–2013), the most frequent OIs were geohelminths (23.5%) and diarrhoeal infection (14.3%). By gender, prevalence was consistently higher in women (p < 0.05) before and after HAART for geohelminths, candidiasis, diarrhoeal infection, bacterial pneumonia and genital ulcer disease but consistently higher in men for TB and Kaposi’s sarcoma (p < 0.05). By age, prevalence was consistently higher in older age groups (>30 years) before and after HAART for oral candida and TB (p < 0.05) and higher in young age groups (<30 years) for malaria and genital ulcers (p < 0.05). By geographical location, prevalence was consistently higher in Eastern and Northern Uganda before and after HAART for diarrheal infection and geohelminths (p < 0.0001).ConclusionsThe frequency and pattern of OIs before and after HAART differs by gender, age and geographical location. Prevalence of geohelminths and diarrhea infection(<1 month) remains high especially in Northern and Eastern Uganda even after HAART and should therefore be given special attention in HIV/AIDS care programmes in these settings.