The objective of the study was to observe the effect of experimental hypodynamy simulating weightlessness in space on the structure, ultrastructure and alkaline phosphatase activity of kidney in Japanese quail (Coturnix coturnix japonica). Two days after hatching, the quails were suspended in special shirts below the cage ceiling so their feet did not touch the floor. They could consume food and water ad libitum. Experimental animals were sacrificed after 14, 21, 28, 35, 42, 49 and 56 days of hypodynamy. Birds of the same age, hatched at the same time, and fed the same diet were used as a control. Samples of kidney were processed for light (LM) and transmission electron microscopy (TEM), and alkaline phosphatase (AP) analysis. Short-term (14–28 days) hypodynamy caused no marked damage to the structure and ultrastructure of kidneys. However, after long-term (35–59 days) hypodynamy, morphological changes were observed in some cells of the proximal and distal tubules. The dying cells in proximal tubules, observed in semi-thin sections by LM, were dark and contained a nucleus of irregular shape. Observation by TEM showed that their nucleus was dark and shrivelled and the electron-dense cytoplasm contained long, dense, rod-shaped mitochondria with thin mitochondrial cristae. Microvilli were present on the apical surface of cells and formed a brush border. Sporadic dying cells were also observed in distal tubules. Large, light vacuoles were found in the cytoplasm of cells of collecting tubules, however, the structure of renal corpuscles and medullary loops remained undisturbed. Microscopical analysis by means of a direct TUNEL reaction on days 35 to 59 of hypodynamy showed a moderate occurrence of cellular apoptosis in the proximal and distal tubules of experimental Japanese quail. The activity of AP in the brush border of the proximal tubules on days 14–29 of hypodynamy was normal in experimental animals and showed no significant differences in comparison with the control. Between days 35 and 59 of hypodynamy a moderate decrease in the content of AP in experimental animals in comparison with the control (P < 0.01) was observed. Our results indicated that long-term hypodynamy caused apoptosis of some cells in the proximal and distal tubules and therefore had a negative effect on the kidney structure. The occurrence of apoptosis was only sporadic. We presume no negative effect on the kidney function and the Japanese quails are capable of further development under the conditions of prolonged simulated weightlessness.