To identify the magnitude of muscle hypertrophy following electrically stimulated exercise in paraplegic subjects, we used quantitative CT (QCT) of the midthigh prior to and following 6 weeks of bicycle ergometry. Three patients who had suffered acute spinal cord injury were examined in this pilot investigation. Average absolute changes in muscle cross-sectional area by QCT were determined to be 10.6 cm2 (p = 0.042) at a distal site located 100 mm above the tibial plateau and 18.8 cm2 (p = 0.019) at a more proximal site (175 mm). Expressed as a percentage increase, these changes were likewise found to be significant. When the total thigh musculature was segmented into anterior and posterior regions, significant increases were observed only among the anterior muscle groups at both the distal and the proximal sites. Muscle hypertrophy as determined by standard anthropometric techniques at 200 mm above the patella was not found to be significant. We conclude that QCT is a valuable technique for discerning changes in muscle size during fitness training and that, in our population, it was capable of differentiating specific muscle compartment hypertrophy secondary to electrical stimulation.