Here we describe the development of a multiple headspace sampling methodology coupled to a programmed temperature vaporizer and a gas chromatograph-mass spectrometer (MHS-PTV-GC-MS) for the determination of 13 polycyclic aromatic hydrocarbons (PAHs) which are considered widespread environmental pollutants. Coupling with the PTV in solvent vent mode made it possible to enrich the analytes present in the headspace through multiple extractions and transfers to the injector previous to the chromatographic run. All parameters affecting the headspace generation, extraction, and stepwise transfer to the PTV were optimised. The method was successfully validated using UHQ-water, for thirteen PAHs, with limits of detection (LODs) in the range of 1.0–11 ng L−1. The method was also validated in saliva, with LODs in the range of 1.4–43 ng L−1. Intra- and inter-day repeatability values expressed as relative standard deviation percentage (RSD) were found to be lower or equal to 8.3% and 12.6%, respectively, in water, and 15.2% and 10.0% in saliva. Furthermore, all calibrations presented good linear behaviour (R2 values >0.98) and fitted to the model according to ANOVA model validation. This method was applied to the quantification of PAHs in 14 saliva samples from 11 subjects, both non-smokers and smokers. PAHs were not detected in saliva from non-smokers and light-smokers above the LODs. However, these compounds could be found in saliva samples from heavy smokers taken right after smoking. A study of the same subjects in saliva samples provided one hour later was also conducted to evaluate the concentration change in time.