Some aromatic amines (AA) have been classified as carcinogens to humans. After entering the body, mainly through tobacco smoke, they can be detected in urine. Thus, their trace analysis as biomarkers in biofluids is of high relevance and can be achieved with gas chromatography (GC–MS), usually after derivatization. This study compares three gas chromatographic methods for the analysis of ten iodinated derivatives of AA: GC–MS in single-ion monitoring (SIM) mode with (1) electron ionization (GC-EI-MS) and (2) negative chemical ionization (GC-NCI-MS), and (3) GC-EI-MS/MS in multiple reaction monitoring (MRM) mode using electron ionization. All methods and most analytes showed good coefficients of determination (R2> 0.99) for broad linear ranges covering three to five orders of magnitude in the picogram-per-liter to nanogram-per-liter range, with one and two exceptions for (1) and (2) respectively. Excellent limits of detection (LODs) of 9–50, 3.0–7.3, and 0.9–3.9 pg/L were observed for (1), (2), and (3) respectively, and good precision was achieved (intra-day repeatability < 15% and inter-day repeatability < 20% for most techniques and concentration levels). On average, recoveries between 80 and 104% were observed for all techniques. Urine samples of smokers and non-smokers were successfully analyzed, and p-toluidine and 2-chloroaniline could be found at significantly (α= 0.05) higher concentrations among smokers.Graphical AbstractSupplementary InformationThe online version contains supplementary material available at 10.1007/s00216-023-04713-8.