Background: The use of fiberoptic endoscopy revolutionized diagnostic gastroenterology. The ultimate diagnosis of malignancy is based on histologic or cytologic criteria. Cytology is a valuable adjunct to biopsy, with the combined yield of the two superior to the yield of either individual technique. Studies done in Basrah evaluated the diagnostic efficiency of brushing cytology, considering endoscopic biopsy results as a gold standard. Aim: To evaluate the clinical utility of endoscopic biopsy and brush cytology versus open biopsies. Material and Methods: Over the period from October 2002 to October 2006, fifty patients were selected with a high suspicion of malignancy by endoscopic examination. Endoscopic biopsy and brush cytology were taken. All the fifty patients proved to have malignancy depending on histopathological finding of open tissue biopsies. The cytology smears were fixed in 95% ethyl alcohol and stained by Papanicolaou stain while the histological specimens processed routinely and stained by hematoxylin and eosin. Analysis done for the results of both techniques and compared with other studies. Results: From the 50 patients with malignancy, brush cytology was positive in 47(sensitivity 94%) and the endoscopic biopsy in 44(sensitivity 88%). Brush cytology diagnosed 3 cases with negative endoscopic biopsy and thus added 6% to the diagnostic yield of malignancy. Conclusion: Brush cytology got higher sensitivity than endoscopic biopsy; however, the two techniques are complementary for the diagnosis of upper gastrointestinal tract malignancies.