The thymus is the central organ of the immunogenesis, the functioning of which determines the protective reactions of the organism. Various stressors can influence the immune organs. One of these factors is exposure to low temperatures. The aim of this research was studying the effect of experimental cold stress on the morphological and functional state of rat thymus using morphometric analysis. The cold exposure was done by placing the rats in individual cages in a refrigeration chamber at a temperature of -10 ± 20 °C for 1 hour at the same time of day for 7, 14, 21, and 30 days. Histological examination of thymus preparations stained with hematoxylin and eosin; on the 7th day after exposure to cold, the area of the cortical substance is significantly reduced compared with the control group, while the area of the medulla tends to increase. Analysis of the cell composition showed an increase in the number of epithelia-reticular cells in the subcapsular zone and a slight decrease in the number of lymphocytes. On the 14th day of exposure, the areas of cortical and medulla and the cortical-cerebral index do not differ from the indicators of intact control. Morphometric counting of cellular elements showed an increase in the number of lymphocytes, epithelia-reticulocytes, and macrophages. After 21 days of the experiment, data on the relative areas of cortical and medulla shows a significant decrease in the rate compared with all the first groups. The counting of cellular elements during this period showed marked changes observed in all morphological and functional zones of the thymus. In the subcapsular zone, there is a sharp decrease in the number of dividing lymphocytes. The number of epithelia-reticular cells is increased relative to the norm. There is frequent detection of apoptotic bodies and fat cells. In the medulla, there is an increase in the number of epithelia-reticulocytes compared with the 7th and 14th day. On the 30th day after exposure, the areas of cortical, medulla, and cortical-cerebral index remained at the same level as on the 21st day. There is a significant decrease in epithelia-reticular cells in the subcapsular zone, a significant decrease in the cortical substance and the cortico-medullary zone compared with all groups, and a significant increase in their number in the medulla. Hassall’s bodies are characterized by pronounced degenerative changes in epithelia-reticulocytes with cellular debris. In the subcapsular zone, a reduced number of cells with mitosis figures is maintained. It was established that as a result of cold stress on days 7, 21 and 30, there is a redistribution of volume and cellular composition, various structural and functional zones, indicating a decrease in the functional activity of the thymus, an increase in the death of lymphocytes by apoptosis, a decrease in mitotic activity, and accumulation of macrophages. Morphological and functional data of the 14th day of the experiment indicate the development of compensatory-adaptive changes in the thymus on the cold effect, manifested in the form of activation of cell division in the cortical substance and the cortical-medullary zone.