Two applications of gas chromatography-mass spectrometry in clinical chemistry, are described, namely the identification and determination of compounds present in biological fluids. For the first application, the biological substances are derivatized to stable forms for gas chromatography and to give appropriate spectra in the mass spectrometer operated in the scanning mode. This method is used for the diagnosis of organic acidurias, different enzyme deficiencies causing congenital adrenal hyperplasia and other disturbances of steroid metabolism, for differentiation between adrenal carcinoma or adenoma, etc. The second application is the use of the mass spectrometer as a very sensitive and selective gas chromatographic detector. This, in combination with stable isotope dilution methods, is the most accurate analytical method in clinical chemistry. The substances are derivatized to forms suitable for gas chromatography and to give a few specific and intense fragment ions in the mass spectrometer operated in selected-ion monitoring mode. Substances that can be detected in this way include steroids, vitamins, prostaglandins, carbohydrates, drugs and pesticides.