The study was done to determine the frequency of etiological spectrum of pancytopenia on the basis of morphologic bone marrow examination as seen in Mulago hospital Uganda. The study design was observational cross sectional study. It was done in the department of Haematology, Mulago Hospital and Makerere University College of Health Sciences (MakCHS) from June 2008 – January 2009. All patients on haematology ward and haematology clinic with pancytopenia from 12 years and above were consecutively recruited. Blood samples were taken from patients after informed consent. The patients below 18 years were consented thorough their parents/guardians. The blood samples were analysed for haemoglobin, total and differential leucocyte counts, platelet count and reticulocyte count. Besides, a peripheral blood smear and bone marrow aspiration/biopsy were also performed. Fifty patients were studied during this period and the most common cause of pancytopenia was megaloblastic anaemia (54%) followed by hyperspleenism (16%), aplastic anaemia(14%). The others included in order of importance were aplastic anaemia, normoblastic erythroid hyperplasia, myelodysplasia. acute leukaemia and multiple myeloma. Severe pancytopenia was mainly due to aplastic anaemia. In conclusion, megaloblastic anemia, hyperspleenism and aplastic anaemia were the most common causes of pancytopenia and aplastic anaemia was the most common cause of severe pancytopenia.