Physical traumas have been implicated as intrinsic risk factors for the progression of urothelial tumours. In stone disease, histologic changes of the urothelium have a wide spectrum. We want to show the importance of biopsies for identification of these changes. In this study, we investigated the histologic changes of the urothelium in stone patients. There were 16 squamous metaplasia, 14 pyelitis follicularis, 5 pyelitis or ureteritis cystica, 4 polypoid pyelitis or ureteritis, 2 encrusted pyelitis in 43 stone patients, and 5 calcium, 2 long-standing struvite and 2 mixed calculi histories were found in 9 of 14 upper urothelial tumour patients. According to our results, it is important to identify the histologic changes of the upper urothelium during stone surgery for possible neoplastic progression in the future. If any suspicious finding is demonstrated, the patient should be enrolled in a follow-up programme or should be transferred to tumour treatment programme. Therefore, we propose to take biopsies of the urothelium in every stone surgery.