Endurance exercise training improves plasma lipoprotein and lipid profiles and reduces cardiovascular disease risk. However, the effect of endurance exercise training, independent of diet and body fat phenotypes, on plasma lipoprotein subfraction particle concentration, size, and composition as measured by nuclear magnetic resonance (NMR) spectroscopy is not known. We hypothesized that 24 weeks of endurance exercise training would independently improve plasma lipoprotein and lipid profiles as assessed by both conventional and novel NMR measurement techniques. One hundred sedentary, healthy 50- to 75-year-olds following a standardized diet were studied before and after 24 weeks of aerobic exercise training. Lipoprotein and lipid analyses, using both conventional and NMR measures, were performed at baseline and after 24 weeks of exercise training. Relative and absolute maximum oxygen consumption increased 15% with exercise training. Most lipoprotein and lipid measures improved with 24 weeks of endurance exercise training, and these changes were consistently independent of baseline body fat and body fat changes with training. For example, with exercise training, total cholesterol, triglycerides, and low-density lipoprotein cholesterol (LDL-C) decreased significantly (2.1+/-1.8 mg/dL, P=.001; -17+/-3.5 mg/dL, P<.0001; and -0.7+/-1.7 mg/dL, P<.0001, respectively), and high-density lipoprotein cholesterol subfractions (HDL3-C and HDL2-C) increased significantly (1.9+/-0.5 mg/dL, P=.01, and 1.2+/-0.3 mg/dL, P=.02, respectively). Particle concentrations decreased significantly for large and small very low-density lipoprotein particles (-0.7+/-0.4 nmol/L, P<.0001, and -1.1+/-1.7 nmol/L, P<.0001, respectively), total, medium, and very small LDL particles (-100+/-26 nmol/L, P=.01; -26+/-7.0 nmol/L, P=.004; and -103+/-27 nmol/L, P=.02, respectively), and small HDL particles (-0.03+/-0.4 micromol/L, P=.007). Mean very low-density lipoprotein particle size also decreased significantly (-1.7+/-0.9 nm, P<.0001) and mean HDL particle size increased significantly with exercise training (0.1+/-0.0 nm, P=.04). These results show that 24 weeks of endurance exercise training induced favorable changes in plasma lipoprotein and lipid profiles independent of diet and baseline or change in body fat.