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BACKGROUND: Hematological abnormalities are common in HIV positive patients. Of these, thrombocytopenia is a known complication which has been associated with progression of disease. However, its magnitude and associated factors in HAART naive HIV positive patients is not known in Ethiopia. Therefore, the aim of this study was to determine the prevalence and associated factors of thrombocytopenia in HAART naive HIV positive patients. METHODS: A retrospective study was carried out among HAART naive HIV positive patients at Gondar University Hospital, Northwest Ethiopia, from September 2011 through August 2012. Socio-demographic variables and immunohematological (platelets and CD4+ T cells) values were carefully reviewed from medical records. Associated factors and outcomes were assessed using logistic regression. RESULTS: A total of 390 HAART naive HIV positive patients with a mean age of 33.65 years and a range of 18-70 years were reviewed. The overall prevalence of thrombocytopenia was 23(5.9%). The mean CD4 count was 288 +/- 188.2 cells/muL. HIV patients whose age >/= 50 years old were 2.5 times more likely to have thrombocytopenia and those patients whose CD4 count < 350 were 2.6 times more likely to have thrombocytopenia than HIV patients whose CD4 count >/=500. However, CD4 count was not statistically associated with prevalence of thrombocytopenia (P > 0.05). CONCLUSION: As CD4 counts of HIV patients decreasing, they have more likely to have thrombocytopenia. Therefore, early diagnosis and treatment of thrombocytopenia in these patients are necessary.