Background Analysis of lipoprotein profile gives important clinical information for lipid-lowering therapy which prevents atherosclerotic diseases. The lipoprotein classes can be isolated from serum with ultracentrifugation, which inevitably consumes a long time and needs large serum volume. We have established a method with anion-exchange chromatography with 1.0 mu L of the injected volume in 5.2min for assay of one sample. Methods One-hundred-forty-one male volunteers without overt diseases were divided three groups (Group 1, non-dyslipidemia with LDL-cholesterol [LDL-C] <120mg/dL and HDL-cholesterol (HDL-C) 40mg/dL; Group 2, borderline dyslipidemia with 120LDL-C<140mg/dL and HDL-C 40mg/dL; Group 3, dyslipidemia with LDL-C140mg/dL or HDL-C<40mg/dL). Their lipoprotein profiles were evaluated by rapid anion-exchange chromatography, which measured concentrations of HDL-C, LDL-C, IDL-cholesterol, VLDL-cholesterol, and other fraction (chylomicron + lipoprotein [a])-cholesterol (other-C). Results The within-day and between-day assay coefficients of variation of lipoprotein cholesterol values were 0.33-4.31% and 2.37-9.19%, respectively. The correlation coefficients between values of HDL-C, LDL-C, IDL-C and VLDL-C by the anion-exchange chromatography and those by ultracentrifugal method were 0.97, 0.92, 0.58 and 0.94, respectively. Group 3 had significantly lower HDL-C and higher concentrations of IDL-C, VLDL-C and other-C than did Group 1. Group 2, borderline dyslipidemia, had significantly higher concentrations of IDL-C and VLDL-C than did Group 1. Conclusion The rapid anion-exchange chromatography assay may be sufficiently applied to the assessment of borderline dyslipidemia.