We examined the effects of bed-rest, recovery and exercise countermeasures on bone density and structure at the distal tibia and radius as measured via high-resolution peripheral computed tomography. 24 subjects underwent 60-days of head-down tilt bed-rest and performed either resistive vibration exercise (RVE; n = 7), resistive exercise only (RE; n = 8) or no exercise (n = 9; 2nd Berlin BedRest Study; BBR2-2). Measurements were performed regularly during and up to 2-years after 60d bed-rest. At the distal tibia marked reductions in cortical area, cortical thickness and bone density but increases in periosteal perimeter and trabecular area were seen (p all<0.001). Recovery of most parameters occurred within 180d after bed-rest. At the distal radius, persistent increases in cortical area, cortical thickness, cortical density and total density and decreases in trabecular area were seen (p all ≤ 0.005). A significant effect of RVE (p = 0.003), but not RE, was seen on cortical area at the distal tibia, with few effects of the countermeasures observed on the remaining parameters. The current study represents the first implementation of high-resolution peripheral computed tomography in bed-rest in male subjects and helps to understand the patterns of bone remodeling due to bed-rest and recovery.