A group of 37 spinal cord injured (SCI) patients underwent bone density measurements at the distal and proximal end of the tibia by a special computed tomography scanner, the OsteoQuant. Fifteen of these patients had follow-up measurements while enrolled in a lower-limb exercise training program with functional electrical stimulation (FES). The pre-exercise measurements revealed a strong correlation (0.88 < or = r < or = 0.90) of trabecular, subcortical, and cortical bone density between the distal and proximal ends of the tibia. The expected bone density loss during the first two years post injury (as calculated from the regression lines of bone density vs. time post injury) amounted to 51.5% for trabecular, 44.2% for subcortical, and 32.7% for cortical bone. No major bone density loss was calculated after 7 years post injury. Analysis of the bone density data during the FES exercise program revealed various degrees of loss. However, the rate of bone loss for this FES exercise group was less than expected from the regression lines. The reduction of bone loss was between 0.2 and 3.3% per year, and was significant (p < 0.05) for all bone parameters at the distal end and for trabecular bone density at the proximal end of the tibia. These bone density measurements revealed a potentially positive effect of FES exercise intervention for the rehabilitation of SCI patients.