Plasma lipoprotein fractions from inbred C57BL/6J mice and outbred ICR mice were prepared by sequential density ultracentrifugation using density ranges that were optimized for separating mouse lipoproteins, or by Superose 6 HR10/30 fast performance liquid chromatography (FPLC). The lipoproteins were characterized by migration behavior in agarose, apolipoprotein (apo) composition, lipid composition, and particle size distribution. Both sequential density ultracentrifugation and Superose 6 FPLC were adapted for the separation of lipoproteins from a single mouse. In the plasma of ICR and C57BL/6J mice, in contrast to human plasma, alpha-migrating high density lipoproteins (HDL) and beta-migrating low density lipoproteins (LDL) had overlapping density ranges. For example, beta-migrating apoB-100 LDL, slow pre-beta-migrating apoB-48 remnants, and alpha-migrating HDL1 were found together in the d 1.02-1.04 g/ml fraction. The d 1.04-1.06 g/ml fraction contained beta-migrating apoB-100 LDL and alpha-migrating HDL1. Large HDL1 that were found at d 1.02-1.06 g/ml were apoE-rich HDL1, characteristic of cholesteryl ester transfer protein-deficient mammals. The d 1.10-1.21 g/ml fraction, in addition to alpha-migrating HDL, included unique slow beta-migrating particles that contained apoE and apoA-I but was deficient in neutral lipids. These slow beta-HDL eluted in the same FPLC fractions as dense alpha-migrating HDL. Compared to ICR mouse plasma, C57BL/6J mouse plasma contained more LDL and less HDL1, which might contribute to the susceptibility of C57BL/6J and the resistance of ICR mice to the development of aortic fatty streak lesions when challenged with an atherogenic diet.