BACKGROUND: Low-carbohydrate, ketogenic diets (LCKD) are effective for weight loss, but concerns remain regarding cardiovascular risk. The purpose of this study was to determine the effect of an LCKD program on serum lipoprotein subclasses. METHODS: This was a randomized, two-arm clinical trial in an outpatient research clinic involving overweight, hyperlipidemic community volunteers motivated to lose weight. Subjects were randomized to either an LCKD (n = 59) and nutritional supplementation (including fish, borage and flaxseed oil), or a low-fat, reduced-calorie diet (LFD, n = 60). The main outcomes were fasting serum lipoprotein subclasses determined by nuclear magnetic resonance analysis. RESULTS: The mean age of subjects was 44.9 years, the mean BMI was 34.4 kg/m(2), and 76% were women. Comparing baseline to 6 months, the LCKD group had significant changes in large VLDL (-78%), medium VLDL (-60%), small VLDL (-57%), LDL particle size (+2%), large LDL (+54%), medium LDL (-42%), small LDL (-78%), HDL particle size (+5%), large HDL (+21%), and LDL particle concentration (-11%). Compared with the LFD group, the LCKD group had greater reductions in medium VLDL (p = 0.01), small VLDL (p = 0.01) and medium LDL (p = 0.02), and greater increases in VLDL particle size (p = 0.01), large LDL (p = 0.004), and HDL particle size (p = 0.05). CONCLUSIONS: The LCKD with nutritional supplementation led to beneficial changes in serum lipid subclasses during weight loss. While the LCKD did not lower total LDL cholesterol, it did result in a shift from small, dense LDL to large, buoyant LDL, which could lower cardiovascular disease risk.