Objective: To investigate changes in lipid, lipoprotein and apolipoprotein profiles in persons with spinal cord injury (SCI) during the first 2 years post-injury, and to determine whether changes in risk profiles were associated with sport activity and/or changes in physical capacity parameters. Design: Risk profiles and physical capacity were investigated in 19 subjects with recent SCI during rehabilitation (t1) and +/- 1 year after discharge from rehabilitation (t2). Main outcome measures: Changes in total plasma cholesterol (TC), high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), triglycerides (TG), apolipoprotein-A1 (ApoA1), apolipoprotein-B (ApoB) concentrations, the ratios TC/HDL-C, LDL-C/HDL-C, ApoA1/ApoB and HDL-C/ApoA1, and physical capacity (maximal isometric strength, sprint power output, maximal power output, aerobic power). Results: Risk profile parameters changed towards more favorable values at t2, except for HDL-C (P = 0.06), TG and HDL-C/ApoA1. Sport activity and changes of the physical capacity were the most important determinants of changes in lipid and (apo)lipoprotein profiles, showing more favorable values with larger increases of the physical capacity and in persons who were physically active. Conclusion: Results show that the lipid and (apo)lipoprotein profiles improve in persons with SCI during the first 2 years post-injury, and that improving the physical capacity or being physically active can improve the lipid and (apo)lipoprotein profiles.