An analytical free flow capillary isotachophoresis (cITP) procedure for the detailed analysis of lipoproteins on commercially available capillary electrophoresis systems has been developed. The technique is based on the specific staining of lipoproteins with the fluorescent lipophilic dye 7-nitrobenz-2-oxa-1,3-diazole (NBD)-ceramide before separation. Prestained lipoprotein samples are applied between leading and terminating buffer and separated into 9 well-characterized subpopulations according to their electrophoretic mobility in the absence of any molecular sieve effect. High density lipoproteins are separated into three major subpopulations: (i) the fast migrating high density lipoprotein (HDL) subpopulation (alpha-HDL, containing mainly apolipoprotein (apo) A-I and phosphatidylcholine, (ii) the subpopulation with intermediate mobility, consisting of particles rich in cholesterol, apo A-II, apo E and C apolipoproteins, and (iii) the slow migrating HDL subpopulation (pre-beta-HDL), containing particles rich in apo A-I, apo A-IV. The majority of HDL-associated lecithin:cholesterol acyltransferase (LCAT) activity is also associated with the last subpopulation. The apo B-containing lipoproteins can be subdivided into three major functional groups. The first represents chylomicron derived particles and large triglyceride-rich very low density lipoproteins (VLDL). The second group consists of small VLDL and intermediate density lipoprotein (IDL) particles, and the third group represents the low density lipoproteins (LDL). Results obtained by the isotachophoretic lipoprotein analysis revealed a good correlation in the range of HDL with routinely used techniques, like lipoprotein electrophoresis, HDL-cholesterol analysis by a precipitation procedure or turbidimetric determination of apo A-I. Similar correlations with other analytical techniques were found for the quantitation of the apo B-containing lipoproteins. Advantages of the isotachophoretic separation compared to zone electrophoresis are the high resolution combined with small sample volumes. Moreover, lipoprotein analysis can be performed directly from whole serum, plasma, lymph and other biological fluids in a short time. With these characteristics analytical capillary isotachophoresis may be a helpful tool for a fast and reliable automated quantitation of lipoprotein subpopulations in the clinical laboratory.