Obesity is associated with multiple conditions that are known to compromise renal function, including hypertension, diabetes, hyperuricemia, and the metabolic syndrome that can independently have a detrimental effect on renal function. The aim of this study was to examine effects of fatty diet induced obesity and melatonin on kidney in female rats by histological and quantative methods. For this aim, 24 rats were randomly divided into 4 groups including Non-obese control (NC group), Obese control (OC group), Nonobese Melatonin (NOM group) and Obese-Melatonin (OM group) groups. In the obese groups, rats, were fed with high fat diet (40% of calories from fat) for 15 weeks. The rats of the non-obese groups were fed with standard, commercial rat diet during the same period. At the end of the 15th week, rats in the melatonin groups started to received daily injections (i.p.) 10 mg/kg melatonin for 6 weeks. At the end of the experiment, a serial sections of kidneys were stained with Hematoxylen-eosin. Glomerular number (Ng) is considered a major determinant of renal function and outcome. Unbiased stereological methods have been used to estimate of Ng. Also histopathological analysis was made on the same sections. Stereological examination of the kidneys showed differences in terms of total kidney volume, volume of cortex, medulla and numerical density of glomeruli among the groups. Light microscopic investigation showed a dilatation in blood vessels and Bowman's space, mononuclear cell infiltration, degeneration in nephrons, including glomerulosclerosis and tubular defects, and an increase in the connective tissue in the kidneys in the OC group. But, both stereological deficits and histological damages detected in OC group recovered in OM group after melatonin treatment. We suggested that a fatty diet is responsible for the rats' obesity and may lead to renal deformities as a result of histopathological changes such as vessel dilatation, tubular defects, inflammation and connective tissue enlargement of the kidney. Also melatonin treatment after obesity may contribute structural and functional healing. © 2013 OMU.