Microgravity environment like space flight or a condition requiring long-term bed-rest increase bone resorption and decrease bone formation, inducing the rapid decrease of bone minerals to osteoporosis. Bone mineral loss increases urinary calcium excretion and the risk of urinary stone formation. To clarify the influence of the conditions on renal stone formation, a 90-day bed rest test was performed to analyze the mechanism of microgravity or bed rest-induced stone formation and prevention by bisphosphonate medication and bed-rest exercise. As the results, renal stone formation was observed in control and exercise groups and no stone was seen in the medication group. In the medication group, urinary calcium excretion and relative supersaturation of calcium oxalate were lower than in the control group throughout the bed-rest and recovery period. Bisphosphonate is useful for the prevention of renal stone formation during space flight and long-term bed-rest.