Previous research supports a role of soy protein in reducing serum lipids, however few studies have involved healthy subjects and/or focused on soy isoflavones. The purpose of this study was to determine the effects of soy protein and isoflavones on serum lipids in healthy young men. Thirty-five subjects consumed milk protein isolate (MPI), low-isoflavone soy protein isolate (low-iso SPI; 1.64 ± 0.19mg iso/day) and high-isoflavone SPI (high-iso SPI; 61.7 ± 7.4mg iso/day) for 57 days each, separated by 4-week washouts, in a randomized crossover design. Serum was analyzed for TC, LDL-C, HDLC, TG, apo B, apo A-I and CRP. There were no significant effects of treatment on individual serum lipids however the ratios of TC/HDL-C, LDL-C/HDL-C and apo B/apo A-I were significantly decreased by both SPI treatments relative to MPI. Results demonstrate that soy protein, regardless of isoflavone content, modulates serum lipid ratios in a direction beneficial for cardiovascular disease risk in healthy young men.