Since cyclophosphamide and busulphan used for therapy of bone marrow transplantation (BMT) can cause urothelial cell changes similar to those found in bladder cancer, comparative morphologic and morphometric urinary cytologic research was carried out, examining 812 urine samples taken from 121 patients undergoing BMT and 60 urine samples from 20 patients with bladder cancer. The morphological results showed some differences in the characteristics of the urinary sediment in urothelial toxicity caused by conditioning therapy in BMT and in bladder cancer; among these were background, cellularity, leukocytes, urothelial cell arrangement, cell shape and size, vacuolization, mitosis, and nucleoli. A comparative morphometric study was also carried out, showing differences regarding cell area, nuclear area and perimeter, and N/C ratio, especially between well-differentiated bladder cancer and urothelial toxicity.