We compared serum lipoprotein cholesterol concentrations in a randomly selected subsample (n = 406) population of children (ages 5 to 17 years), as measured by the heparin-Ca2+ and the heparin-Mn2+ precipitation methods. Statistical analysis showed significant differences between results by these methods, especially in values for VLDL- and HDL-cholesterol (mean difference: VLDL-cholesterol, -61 mg/L; HDL-cholesterol, + 108 mg/L). Lipoprotein electrophoretic data indicated that estimating VLDL-cholesterol from serum triglyceride concentrations invariably resulted in higher values for children with an extremely faint pre-beta-lipoprotein band. Among the HDL-subfractions, 14 to 20% of HDL2 was precipitated by heparin-Mn2+ despite the presence of 80 g of albumin per liter. Heparin affinity chromatography of HDL2 in the presence of Ca2+ and Mn2+ showed an interaction of apolipoprotein E-containing HDL2 subfraction only in conditions involving Mn2+. The heparin-Ca2+ procedure precipitated the equivalent of 2 g of beta- plus pre-beta-lipoprotein cholesterol per liter from serum, with no detectable apolipoprotein B in the supernate. We conclude that these precipitations are affected by cation specificity and by differences in lipoprotein makeup of a given individual or population group.