A procedure for the determination of very low polycyclic aromatic hydrocarbons (PAHs) concentrations in sediment samples has been developed by gas chromatography-quadrupole ion trap mass spectrometry (GC-QIT MS) after extraction with dichloromethane and purification by using silica gel cleanup. Identification and quantification of analytes were based on the selected ion storage (SIS) strategy using deuterated PAHs as internal standards. In order to search out the main factors affecting the SIS mass spectrometry efficiency, four MS parameters, including target total ion count (TTIC), waveform amplitude (WA), transfer line (XLT) and ion trap temperatures (ITT) were subjected to a complete multifactorial design. The most relevant parameters obtained (TTIC and WA) were optimized by a rotatable and orthogonal composite design. Optimum values for these parameters were selected for the development of the method involving PAH determination in sediment samples. The optimized method exhibited a range of 111-760% higher signal-to-noise (S/N) ratios for PAHs in comparison with the method operated by the default conditions, demonstrating that the multifactorial optimization contributed to substantially improve the sensitivity of the GC-QIT MS determination. The accuracy of the method was verified by analyzing NWRI EC-3 certified reference material (Lake Ontario sediment). The selectivity, sensitivity (limits of quantification were in the range of 0.02-11.0 ng g(-1)), accuracy (recoveries >or=77%) and precision (RSD<or=30%) obtained were quite adequate for the determination of very low target PAHs in sediment samples. The established method was then applied to determine 16 PAHs in river sediments from the Metropolitan Region of Curitiba, Brazil. Two selected sediment samples were analyzed, one from the Canguiri River (a slightly urbanized area), and the other from the Iguaçu River (a heavily urbanized area), illustrating the capabilities of the method to detect PAHs at the threshold concentrations necessary to classify the sediments as well as the status of contamination.