Cholesterol is the precursor of many compounds with functions in the physiology and metabolism of the organism. Methods for the multicomponent analysis of these compounds and their metabolites (metabolomics) are needed to improve our understanding of their roles in different species, organs, cells and metabolic situations and to clarify structure/activity relationships. This review discusses methods based on combinations of ion exchange and reversed-phase separations for sample preparation with derivatization and "charge-tagging" for chromatography-mass spectrometry in qualitative and quantitative characterizations of oxysterol, bile alcohol, bile acid, and steroid hormone metabolomes. Advantages, disadvantages and potential improvements for high-throughput applications are briefly discussed. (C) 2010 Elsevier Inc. All rights reserved.