The introduction of the highly active antiretroviral therapy (HAART) in 1996 has drastically reduced the morbidity and mortality associated with the HIV infection. Although short term toxicities of the antiretroviral drugs are being reported, there's dearth of data on their long term complications, particularly in sub-Saharan Africa. This study was designed to identify hematological and metabolic toxicities in HAART-experienced patients in our facility from January 2000 to December 2009. Patients on HAART for ≥ 2 weeks, and have at least one abnormal laboratory result (hemoglobin < 10.0 g/dl, white blood count < 4,500/ mm 3 , absolute neutrophil cell count < 1,400/ mm 3 , platelets < 150,000/mm 3 , alanine transaminase > 40 iu/L, creatinine > 130 mmol/L, fasting blood sugar > 6.7mmol/L, fasting cholesterol > 2.5mmol/L, fasting triglyceride > 0.5mmol/L) on follow-up evaluations were studied. Of 3641 patients, 357 (9.8%) comprising 231 females (64.7 %) and 126 males (35.3%) with respective mean ages of 36.16 ± 9.06 years and 42.56 ± 9.36years had hematological and metabolic toxicities, due mainly to zidovudine/lamivudine/nevirapine (51.8 %), stavudine/lamivudine/nevirapine (16.5%), and truvada/nevirapine (10.4%). Common laboratory toxicities were elevated alanine transaminase enzyme (39.8%), leucopenia/neutropenia (38.0%), elevated creatinine level (12.3%), and low hemoglobin (11.5%), although the most severe toxicity was grade 4 anemia. Risk factors for these toxicities were: young age, female gender, pre-and on-ART CD4+ > 250 cells/µL. In conclusion, the current first line antiretroviral regimens produced various forms of hematological and metabolic toxicities, except glucose or lipid abnormalities.