Exercise affects the vertebrate skeleton via biomechanical and biochemical stress. Exercise‐induced strains can elicit increased primary bone formation and/or secondary remodelling of limb bones. Exhaustive exercise results in high lactic acid loads, which may require buffering by bone mineral and thus influence bone remodelling. Cardiac shunting in crocodylians is thought to divert protons to the enteric circulation and reduce acidity of systemic arterial blood in exercise‐stressed animals. We subjected juvenile alligators to exhaustive exercise (running or swimming) every other day for 17 months, and compared their skeletons with those of sedentary controls. Prior to exercise training, half the animals in each group had their left aorta surgically occluded, thus rendering them incapable of cardiac shunting. Alligators were fed twice weekly, and given injections of fluorescent dyes to determine bone deposition rates. Preliminary data show that bone formation rate at the femoral midshaft correlates with whole‐body growth rate in all groups, but is significantly higher in treadmill runners. This suggests that terrestrial, but not aquatic, exercise stimulates bone growth. Loss of cardiac shunting did not affect bone formation or remodelling, which suggests cardiac shunting does not protect skeletal integrity in alligators. Funded by NSF IOB 04445680 to JWH. TO and JMB supported by NIH 2T32AR047752.