Apolipoprotein-B-48 is a structural protein exclusively associated with post-prandial lipoproteins (chylomicrons). Apolipoprotein B-48 would be a useful marker to monitor the kinetics of chylomicrons in vivo, however, its quantitation is limited because of a low concentration in plasma and lack of specific antibodies. Dynamic sieving capillary electrophoresis (DSCE) has recently become widely available for the separation of nanomolar quantities of proteins by size and electrophoretic mobility. Here we describe the potential of DSCE to accurately quantitate apolipoprotein mass in one ml of plasma. Separation of human serum apolipoproteins was achieved through an uncoated fused silica glass capillary column with quantitation based on area response at 220 nm. The retention times of human apolipoprotein B-48, apolipoprotein B-100 and albumin were 8.96 min +/- 0.57%, 10.21 min +/- 0.72%, and 6.56 min +/- 0.4%, respectively (phase-standardized to internal reference). A significant correlation (r = 0.99) was observed between apolipoprotein concentrations and peak area response for mass ranges of 30-40 micrograms/ml. DSCE provides an alternative method for quantifying apolipoprotein B-48 and therefore, may be useful for studying postprandial lipoprotein metabolism.