Two cases of urinary tract malakoplakia, one in right kidney and the other one in urinary bladder, were reported. Both cases affected middle-aged female patients with long-term urinary tract infection. Their clinical presentation simulated a neoplasm. The diagnosis entirely depended on pathologic examination. The former case also extensively involved the retroperitoneum, liver and duodenum. The latter case was unusually associated with Pseudomonas infection. Electron microscopy showed that the morphogenesis of Michaelis-Gutmann bodies occurred within the phagolysosomes. Initially, small myelin-like figures-containing phagolysosomes were undergoing to fuse to form a large one. Then, the membranous fragments and myelin-like figures served as nucleation sites. The nucleation sites could be multiple in the same phagolysosome. Needle shaped crystalline material began to deposit by unknown mechanism. Finally, mature Michaelis-Gutmann bodies were well formed. But no bacteria were identified. The two cases were successfully managed with surgical resection then sulfamethoxazole-trimethoprim treatment. Finally, it was emphasized that frozen section of tumor biopsy avoided unnecessary radical surgery in the latter case.