A cohort of human immunodeficiency virus (HIV)-positive patients presenting to a quaternary hospital in KwaZulu-Natal, South Africa over a period of one year was identified and morphological analyses of their bone marrow aspirates and trephine biopsies (BMAT) undertaken. Aim: To compare and contrast the bone marrow morphological features of antiretroviral (ARV)-naïve and ARV-experienced HIV-positive population with cytopaenias; correlate the findings with CD4 counts; and, draw conclusions on whether ARV are associated with specific bone marrow (BM) findings. Method: Aspirate and trephine biopsy examinations to assess dysplasia of cell lineages, architectural changes, granulomas or infiltrates were performed by light microscopy. Results: 74 BMAT were examined, of which 24 were from the ARV-naïve cohort and 50 from ARV-treated cohort. Within granulomas, higher rates of marrow infiltration by acid-fast bacilli was present in the ARV-naïve cohort than the ARV-experienced cohort (6/10 (60%) versus 9/26 (35%), respectively). Higher rates of pure red cell aplasia (PRCA) were detected in the ARV-experienced than the ARV-naive cohort (14% versus 4%, respectively). No difference was seen in morphological features and overall dysplasia rates (70% and 71% of ARV-naïve and ARV-experienced cohort, respectively). At CD4 > 200 cells/ul, higher rates of dysplasia were seen in the ARV-naïve cohort (3/3 (100%) than in the ARV-experienced cohort (13/20 (65%)). Conclusion: Similar dysplasia rates and morphological features in both cohorts suggest ARVs do not cause myelodysplasia. BM tuberculosis is more frequently detected in granulomas of ARV-naïve than ARV-experienced samples. ARVs are implicated in causation of PRCA.