Aims Electromagnetic waves (EMF) are powerful waves that have always been used in advanced industries. The daily effects of waves are evident in today’s life. This research aims to investigate the effect of EMF on the healthy tissue of the kidney, bladder, and ureter. Methods & Materials In this experimental study, 100 rats were randomly selected and divided into 2 equal groups. The treatment group included 50 rats influenced by EMF waves (1 mT) for 8 hours daily over 8 weeks. The control group, including 50 rats without irradiation was kept for 8 weeks. At the end of the period, all rats were killed via the euthanized method, and the kidney, bladder, and ureter were sampled and after tissue passage, were stained by hematoxylin and eosin stain and terminal deoxynucleotidyl transferase (TdT) nick end labeling methods. Findings The histopathological changes and cell damage in the kidney, bladder, and ureter included atrophy and necrosis of cells, disorganization, hyperemia, and bleeding in the covering, muscular, and connective tissues. Meanwhile, in the kidney tissue, from the point of view of the induction of ptosis, a large part of the nephrons undergo apoptosis. The results of the statistical analysis were obtained via the Mann-Whitney test method. The result was P≥0.05, indicating a statistically significant effect. Conclusion It is recommended that exposure to EMF for a long time must be avoided.