Methyl tert-butyl ether (MTBE) is a relatively new anthropogenic factor of environmental pollution. It is already known that it is an environmentally hazardous substance that has a toxic effect on the human body. The purpose of the research is to study the effect of MTBE on the structural organization of the kidneys of research animals. White outbred rats were involved into the research, which were treated with 500 mg/kg MTBE in an oil solution, which was administered intragastrically using a gastric catheter. Structural changes in the kidneys on the 3rd, 8th, 15th, 22nd and 60th day of the research were studied by means of light-optical and electron microscopy. The obtained material was processed statistically using the parametric Student's test and the nonparametric Kolmogorov-Smirnov test in accordance with the principles of variation statistics. During the runtime of the research, we have clearly defined the staging of changes in the structural organization of the kidney and the dependence of their severity on the duration of MTBE action. With short-term exposure (3, 8 and 15 day of the research), the weight of the kidneys and other organometric parameters do not differ from those in the control group. In the initial stages of MTBE action, we have observed reactive changes, which are clearly manifested in the structures of the filtration barrier (3rd day), and with an increase in the observation period (8th day) they spread to the epithelial cells of the proximal tubules. After 15 days of MTBE action, against the background of pronounced compensatory-adaptive events, we have noticed the development of dystrophic-destructive processes in the renal corpuscles and in the proximal tubules. There are structural signs of enhanced synthetic activity in the mesangial cells. On the 22nd day of the experiment, the morphometric index of the mass and linear dimensions of the kidneys increase in comparison with the control group. There are structural signs of atrophy and hypertrophy processes in the nephrons. There are progressive changes in the tubular apparatus of the kidneys in comparison with the previous period of the research. Long-term action of MTBE (60 days) causes further deepening of dystrophic and destructive changes in all parts of the nephron, which differ in intensity. It has been proved that MTBE has a negative effect on all structural components of the nephron, which leads to disorganization of the filtration and reabsorption of kidney apparatus and significant development of the connective tissue, which causes the development of sclerosis. Besides, it has been proved that MTBE has an apparent nephrotoxic effect and the degree of damage to the structural components of the kidney is determined by the duration of the body's contact with this toxic substance.