The basic principle in quantitative analysis by mass spectrometry is the measurement of a signal representative of the mass of the analyte relative to a known amount of an internal mass standard. To ensure that the signal is representative of the particular substance to be measured and not a result of some other substance in the biological matrix, a range of analytical methods have been employed. Combination of mass spectrometry with chromatographic (gas or liquid) separations and selective chemical derivatization frequently allows quantification of substances at the ppm and ppb level. Below the ppb level, new problems arise due to mass spectrometric sensitivity and chromatographic separation resolution with resulting debate regarding the specificity and significance of quantitative data. Successful high sensitivity (ppt) plasma analysis of the pineal hormone melatonin is described and critically compared with conflicting analytical data. A second area of application of quantitative mass spectrometry is the establishment of absolute or definitive reference measurements which require rigorous error minimization. Conflicting results published by two laboratories regarding methods for the definitive measurement of serum cholesterol are compared.