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High-performance liquid chromatography (HPLC) or capillary electrophoresis (CE) is particularly suited to the separation and analysis of a wide range of biological compounds. When investigating such compounds in complex matrices (e.g., blood, tissue, urine, foods), specificity of the detection method becomes an important issue. This can be overcome by extensive purification procedures before HPLC or CE analysis, but at the cost of a lot of effort and often unknown losses during the extraction and purification procedures. Such losses can be overcome by the addition of isotopically labeled internal standards, subject to their availability. The coupling of HPLC or CE with mass spectrometry provides a very specific method of detection. Compounds are transferred as ions to the gas phase by two types of spraying technologies, electrospray ionization (ESI) and heated nebulizer-atmospheric pressure chemical ionization. Although the mass-to-charge ratios of the molecular ions can be used to provisionally identify a compound, full confirmation of structure requires collision-induced dissociation and analysis of the resulting fragment ions. Combination of specific parent ion-daughter ion pairs allows for the quantitative measurement of isoflavones in the 1-5 pmol range with coefficients of variation for duplicate samples in the range of 5-9%. CE places greater demands on the mass spectrometer than does HPLC, because it generates narrow peak widths. A mass spectrometer with a scanning quadrupole analyzer does not enable full exploitation of the power of CE; in this context, an instrument with an ESI interface and a time-of-flight analyzer is ideal.