The aim of this work was to determine structural and functional changes in a small intestine of rats after morning and evening administration of melatonin in obese animals during the spring-autumn photoperiod (12L:12D). The obesity was caused with a high-calorie diet for 6 weeks. After that, morning or evening melatonin administrations were given to normal and obese animals at a dose of 30 mg/kg for 7 weeks. After that, paraffin sections of the small intestine were made, on which a state of the mucosa, enterocytes and goblet cells in crypts was morphometrically and visually examined under a microscope. It has been shown, that obesity causes swelling and an increase of thickness of a mucosa, reduction of crypts, a decrease of activity of enterocytes and goblet cells of the small intestine. Introduction of melatonin to animals without obesity causes an increase in thickness of mucosa and a decrease in area of goblet cells. Additionally, after morning melatonin administration a depth of crypts and a height of enterocytes increases. Morning administration of melatonin to obese animals partially recovers crypts and their goblet cells, but doesn't prevent mucosal edema and worsens a state of enterocytes. The evening administration of melatonin partially normalizes all structural changes, caused by obesity. It was concluded, that melatonin may partially correct morpho-functional changes in the small intestine, caused by obesity in the spring and autumn seasons. The evening administration of melatonin to animals with obesity is more effective, than morning administrations. Also, the evening administration of melatonin causes fewer changes in the small intestine of animals without obesity, compared with morning administration.