Lipoprotein a [Lp(a)] has been recognized as a significant marker for premature coronary heart disease (CHD). In this paper, we present the results of Lp(a) analysis based on capillary zone electrophoresis (CZE). CZE separation of Lp(a) and its reduced species, lipoprotein a- [Lp(a-)] and apolipoprotein a [apo(a)], was accomplished using 50 mM borate buffer containing 3.5 mM sodium dodecyl sulfate (SDS) and 20% (v/v) acetonitrile (ACN). Low density lipoprotein (LDL) and high density lipoprotein (HDL) were separated under the same buffer conditions. The electrophoretic mobilities of both Lp(a) and Lp(a-) were found to be different from that of LDL. Benzyl alcohol (BA) and methanol (MeOH) were used as electroosmotic flow markers. BA molecules associated with Lp(a-) and LDL to enhance their UV absorbance, but did not change their effective electrophoretic mobilities. Our results show that CE is a very efficient and effective technique for lipoprotein analysis.