We have examined the effect of circadian disturbances induced by night shifts (NSs) on the phenotypes of the tibiae and abdominal adipose tissues (ADTs) in a mouse model by using in vivo micro-computed tomography (micro-CT). We found that the volumes of total and visceral ADTs in the night-shifted group of mice were significantly larger (69 and 92%, respectively) than those in the control. The mean polar moment of inertia, cross-sectional thickness, and bone mineral density of the cortical bone in the night-shifted group of mice were less (13, 5, and 3%, respectively) than those in the control. Moreover, the volume and the thickness of growth plates (GPs) of the tibiae in the night-shifted mice were significantly smaller (22 and 20%, respectively) than those in the control. Taken together, our results indicate that disturbances in the mouse circadian rhythms induced by NSs affect the morphological characteristics of cortical bone, the volume and the thickness of GPs, and the volume of ADTs.