Design: Cross-sectional. Objectives: (1) To determine the effects of the level of spinal cord injury (SCI) on skeletal muscle, intramuscular fat (IMF) cross-sectional areas (CSAs) and relative IMF; (2) to determine the relation, if any, of spasticity to each of these variables after incomplete SCI. Settings: In-patient study at the Shepherd Center, Atlanta, GA, USA. Methods: Thirteen individuals with incomplete SCI were classified according to their level of injury into a high level of injury group (HLI, C5-C7, n ¼ 8) and a low level of injury group (LLI, T12-L2, n ¼ 5). Spasticity was determined for thigh muscles using a modified Ashworth scale at 6 weeks post-injury. T1-weighted magnetic resonance (MR) images were taken 6 weeks post-injury to measure thigh skeletal muscle and IMF CSAs. Results: Spasticity was significantly evident in the HLI group compared to the LLI group (P ¼ 0.023). Six weeks post-injury, muscle CSA was 103718 cm 2 in the HLI group and 80720 cm 2 in the LLI group (P ¼ 0.042). Relative IMF was 3.672.0% in HLI and 7.574.0% in LLI (P ¼ 0.021). Additionally, spasticity accounted for 54% of the variability in muscle CSA for all subjects (r 2 ¼ 0.54, P ¼ 0.006). Conclusions: Spasticity may be an important factor in defending skeletal muscle size and indirectly preventing IMF accumulation early after incomplete SCI.