BACKGROUND The last decade brought a deeper understanding of gastrointestinal stromal tumors (GIST). The cell of origin is the pacemaker cell of Cajal which has an intermediate function between the autonomic nervous system and the smooth muscle cells of the gastrointestinal tract. These cells express KIT/CD117 and less consistently CD34. Based on this facts new diagnostic and therapeutic methods have been developed. In this study we applied the current immunohistochemical methods on tumor tissue previously diagnosed as stromal tumor. METHODS Histological specimens diagnosed as GISTs during 3 years (2005-2007) in the Department of Pathology, Tikur Anbessa Hospital, Addis Ababa, Ethiopia were reviewed and the available blocks were used for immunohistochemical assessment of KIT/CD]17 and CD34 expression. RESULTS Tumor specimens of 17 patients were analyzed histologically. Most tumors were purely spindle celled (82%), the rest were mixed (spindle cells/epithelioid cells). Blocks of 14 tumors allowed immunohistochemical investigation. KIT/CD117 positivity could be shown in 11 of 14 tumors, CD34 positivity in 9 of 13 tumors. In contrast to the reported cases from Western countries Ethiopian patients with GISTs were younger, their tumors were larger and the most common sites were small and large intestine, not the stomach. CONCLUSIONS GISTs became probably not more common but gave rise to increased interest during the last decade because of growing understanding of origin, behavior, and molecular mechanism. GISTs seen in Ethiopia differ from those reported in Western countries in age, size and location within the gastrointestinal tract.