BACKGROUND: The size reduction of low density lipoproteins(LDL) particles has been found associated with coronary artery disease(CAD), but the analysis of LDL subfractions is time consuming(over 24 hours) and technically demanding such as density gradient ultracentrifugation or gradient polyacrylamide gel electrophoresis(PAGE). In this study, the association between LDL subfractions and CAD was investigated using the new method for the separation of LDL subfractions, commercially available continuous disc PAGE. METHODS: LDL subfraction profiles were investigated in two groups(97 patients with CAD proven angiographically and 109 healthy controls) using Lipoprint LDL System(Quantimetrix Co., Redondo Beach, CA, USA). Seven LDL subfractions(from LDL-0 to LDL-6) can be identified with a specific electrophoretic mobility(Rf) relative to the HDL fraction. The relative percentage of the area under the curve(AUC) of each LDL band was multiplied by its band number and the sum of the relative AUC of all LDL bands percent was calculated to produce a final LDL score. RESULTS: Mean LDL score was significantly higher in CAD patients than in controls(2.09+/-0.77 and 1.01+/-0.38, respectively, P<0.0001). There was a significant association between the polydispersity of LDL subfractions and the presence of CAD(P=0.01). LDL score was highly correlated with triglyceride(r=0.330, P=0.0001). LDL score was the significant discriminators between control and CAD groups(F=168.3, P=0.0001). There was no significant association between LDL score and the severity of CAD. CONCLUSIONS: Lipoprint LDL System is an easy and quick method for routine assessment of LDL subfractions. LDL score was the best individual discriminant risk factor for CAD.