The aim of this study was to determine the copy number changes of chromosomes 7, 17, 3p, and Y in a non-neoplastic tubular epithelium in end-stage kidney disease (ESKD). Seventeen kidneys from 11 patients with ESKD were retrieved from the archive files. Non-neoplastic kidney tissue in these cases was examined separately. Tissues containing papillary adenomas (PA), clear (CRCC) and papillary renal cell carcinomas (PRCC), and myxoid liposarcoma (LPS) were examined using the same probes and compared with non-neoplastic tissue. Tubular changes in the kidney parenchyma were classified into three types: (1) The vast majority of tubules were entirely atrophic; (2) Several tubules were hyperplastic, i.e., tubules with undifferentiated large epithelial cells, in which it was impossible to establish the specific type of a renal tubulus; (3) Dysplastic tubules were dilated, sometimes wrinkled. The basal membranes were lined by large eosinophilic epithelial cells with polymorphic nuclei and pseudostratification. Nucleoli were clearly visible. These tubular changes were multifocal with a haphazard distribution within the atrophic parenchyma. PA were detected in nine patients, of whom eight patients also revealed an additional tumor type(s) (4x CRCC, 3x PRCC, 1x PRCC, and CRCC). One patient had a CRCC only, another had a combination of PRCC and LPS. Chromosomal abnormalities were found in the second and third group of tubular changes, i.e., in hyperplastic and dysplastic tubules. Trisomy of chromosome 7 was detected in six cases, whereas trisomy of chromosome 17 in eight cases. A combination of both trisomies was found in five cases. Loss of chromosome Y was found in two cases. Fluorescence in situ hybridization on tissues containing papillary adenomas, renal cell carcinomas, and liposarcoma revealed expected results, i.e., trisomy of chromosomes 7 and 17 in all PAs and PRCC. No gains were present in CRCC and LPS. Loss of Y was found in six PA, five PRCC, and one LPS; loss of X was found in two CRCCs. We suggest that chromosomal changes typical of the papillary renal cell lesions, i.e., trisomies of chromosomes 7 and 17, are very frequent in non-neoplastic parenchyma of the end-stage kidney, and they have a tendency to a multifocal occurrence.