Severe muscle atrophy occurs rapidly following traumatic spinal cord injury (SCI). Previous research shows that neuromuscular or 'functional' electrical stimulation (FES), particularly FES-cycle ergometry (FES-CE) can cause muscle hypertrophy in individuals with chronic SCI (> 1 year post-injury). However, the modest degree of hypertrophy in these already atrophied muscles has lessened earlier hopes that FES therapy would reduce secondary impairments of SCI. It is not known whether FES treatments are effective when used to prevent, rather than reverse, muscle atrophy in individuals with acute SCI. This study explored whether unloaded isometric FES contractions (FES-IC) or FES-CE decreased subsequent muscle atrophy in individual with acute SCI (< 3 months post-injury). Twenty-six subjects, 14-15 weeks post-traumatic SCI, were assigned to control, FES-IC, or FES-CE against progessively increasing resistance. Subjects were involved in the study for 3 or 6 months. Total body lean body mass (TB-LBM), lower limb lean body mass (LL-LBM), and gluteal lean body mass (G-LBM) were determined before the study, and at 3 and 6 months using dual energy X-ray absorptiometry (DEXA). Controls lost an average of 6.1%, 10.1%, 12.4%, after 3 months and 9.5%, 21.4%, 26.8% after 6 months in TB-LBM, LL-LBM and G-LBM respectively. Subjects in the FES-IC group consistently lost less lean body mass than controls, however, only 6 month G-LBM loss was significantly attenuated in this group relative to the controls. In the FES-CE group, LL-LBM and G-LBM loss were prevented at both 3 and 6 months, and TB-LBM loss was prevented at 6 months. In addition, FES-CE significantly increased G-LBM and LL-LBM after 6 months of training relative to pre-training levels. Within the control group, there was no significant relationship between LL-LBM loss (3 and 6 months) and the number of days between injury and baseline measurement. In summary, this study shows that FES-CE, but not FES-IC, training prevents muscle atrophy in acute SCI after 3 months of training, and causes significant hypertrophy after 6 months. The magnitude of differences in regionalized LBM between controls and FES-CE subject raises hopes that such treatment may indeed be beneficial in preventing secondary impairments of SCI if employed before extensive post-injury atrophy occurs.