Abstract Described is a liquid chromatography–mass spectrometry (LC–MS) procedure for the determination of hydroxylated biotransformation products of polycyclic aromatic hydrocarbons (PAH) in the human gastrointestinal tract. The formation of hydroxylated PAHs was monitored upon incubation of PAHs with colon microbiota from the Simulator of the Human Intestinal Microbial Ecosystem (SHIME). The analytical method consisted of a biomass removal step followed by a solid phase extraction (SPE) step using C18 packed columns to remove non-digested food compounds and microbial metabolites that interfere with the detection of the target compounds. For quantification, 9-hydroxyphenanthrene 13 C 6 was used as the internal standard. The detection limits of the hydroxylated PAHs were generally in the range 0.36–14.09 μg l −1, based on a signal/noise ratio of 3:1. The recovery of hydroxylated PAHs in intestinal suspension was variable ranging from 45 to 107%, with relative standard deviation (R.S.D.) between 5 and 17%. The analytical procedure was used to show the microbial production of 1-hydroxypyrene and 7-hydroxybenzo( a)pyrene, metabolites that may give colon incubated PAHs bioactive properties.