in lower vertebrates. Metabolism of cholesterol to bile acids/bile alcohols is of major importance for the maintenance and regulation of cholesterol homeostasis. Depending on their structure, bile acids/bile alcohols can be ligands to nuclear receptors with different regulatory functions in animals, including even Caenorhabditis elegans ( 1 ). Bile acids can be formed in some marine microorganisms ( 2 ). These fi ndings have increased interest in methods for specifi c and sensitive analysis of bile acids.Conjugated forms of bile acids/bile alcohols in bile (bile salts) are essential participants in the absorption of lipids and lipid soluble compounds. Studies of this function, bile secretion, enterohepatic circulation, levels in blood, urine, and feces required methods for analysis of bile acids. In 1844, M. von Pettenkofer described his classical color reaction between cholic acid(s) and sugar in conc. sulfuric acid. During the subsequent 100 years, the reaction was modifi ed in numerous ways. This period is described by Sobotka ( 3, 4 ), who pointed out the discrepancies between the poor quality of the analytical methods of his days and the better understanding of bile acid physiology and pathology. He made the following remarks, well worth considering today:"The value of a method lies not only in its specifi city but also in the ease with which interfering factors may be specifi cally removed. To test the usefulness of a method, it is insuffi cient to demonstrate that solutions of the pure substance yield correct results and that known amounts of the substance, when added to biological material, may be completely recovered. It is absolutely necessary to prove that the analytical reaction given by the biological material or extract is due to the substance for which one tests. The unequivocal identifi cation of this substance, in amounts consistent with the analytical data, should alAbstract The formation of bile acids/bile alcohols is of major importance for the maintenance of cholesterol homeostasis. Besides their functions in lipid absorption, bile acids/bile alcohols are regulatory molecules for a number of metabolic processes. Their effects are structure-dependent, and numerous metabolic conversions result in a complex mixture of biologically active and inactive forms. Advanced methods are required to characterize and quantify individual bile acids in these mixtures. A combination of such analyses with analyses of the proteome will be required for a better understanding of mechanisms of action and nature of endogenous ligands. Mass spectrometry is the basic detection technique for effl uents from chromatographic columns. Capillary liquid chromatography-mass spectrometry with electrospray ionization provides the highest sensitivity in metabolome analysis. Classical gas chromatography-mass spectrometry is less sensitive but offers extensive structuredependent fragmentation increasing the specifi city in analyses of isobaric isomers of unconjugated bile acids. Depending on the nature of the bile acid/bile alc...