This paper describes the application of synchrotron radiation microtomography to osteoporosis research. By taking advantage of the high intensity, collimation, and monochromaticity of synchrotron radiation, we have been able to image the three-dimensional trabecular bone structure in living rats, thus providing serial data on the earliest architectural changes that occur with estrogen loss. Results from these in vivo animal experiments demonstrate that one of the earliest manifestations of estrogen loss, in addition to a decrease in the amount of trabecular bone, is decreased connectivity. We demonstrate that estrogen replacement therapy, when initiated soon after significant changes have occurred, restores bone mass to baseline levels but does not recover the trabecular connectivity. Even without an associated recovery in trabecular connectivity, finite element calculations on the three-dimensional images suggest that estrogen recovers the original structural modulus of elasticity. We believe the recovery of the elastic properties is due to an increase in trabecular thickness above baseline values.