A method is described for the fast routine determination of the anti-HIV drug saquinavir and its pentadeuterated analogue [2H5] saquinavir in the plasma of healthy volunteers. The method is based on high-performance liquid chromatography (HPLC)/atmospheric pressure positive-ion chemical ionization (APCI) mass spectrometry, with a stable labelled form of saquinavir (13C62H315N) as internal standard. Automated solid-phase extraction in combination with short-column HPLC and multiple reaction monitoring is employed for high selectivity and sensitivity, and this also permits rapid quantification (the run time per sample is 1.5 min) over the range of 0.4–200 ng ml−1 with excellent accuracy and precision. Up to 200 samples per analyst per day can be analysed. This assay methodology illustrates the versatility of APCI tandem mass spectrometry, in conjunction with high-speed HPLC, for the fast routine quantification of drugs in the nanograms per millilitre range, which is essential for clinical pharmacokinetic studies.