The aim of the present study was to describe bone loss of the separate compartments of trabecular and cortical bone, as well as changes in bone geometry of a large number of spinal cord injured (SCI) individuals. Eighty-nine motor complete spinal cord injured men (24 tetraplegics and 65 paraplegics) with a duration of paralysis of between 2 months and 50 years were included in the study. Distal epiphyses and midshafts of the femur, tibia, and radius were measured by peripheral quantitative computed tomography. The same measurements were performed in a reference group of 21 healthy able-bodied men of the same age range. In the femur and tibia, bone mass, total and trabecular bone mineral density (BMDtot and BMDtrab, respectively) of the epiphyses, as well as bone mass and cortical cross-sectional area of the diaphyses, showed an exponential decrease with time after injury in the spinal cord injured subjects. The decreasing bone parameters reached new steady states after 3-8 years, depending on the parameter. Bone mass loss in the epiphyses was approximately 50% in the femur and 60% in the tibia, while the shafts lost only approximately 35% in the femur and 25% in the tibia. In the epiphyses, bone mass was lost by reducing BMD, while in the shaft bone mass was lost by reducing cortical wall thickness, a process achieved by endosteal resorption advancing at a rate of about 0.25 mm/year within the first 5-7 years after injury. Except for a slight transient decrease in cortical BMD of the femoral and tibial shaft during the first 5 years after the spinal cord lesion, cortical BMD of the spinal cord injured subjects was found to be at reference values. Bone parameters of the radial epiphysis in paraplegic subjects showed no deficits compared to the reference group. Furthermore, a trend for an increased radial shaft diameter suggests periosteal apposition as a consequence of increased loading of the arms.