An in-situ derivatization thermal desorption method followed by gas chromatography and time-of-flight mass spectrometry (IDTD-GC-TOFMS) was developed for determination of polar organic compounds together with non-polar compounds in one measurement. Hydroxyl and carboxyl groups of compounds such as anhydrous sugars, alcohols and phenols, fatty acids and resin acids are targets of the derivatization procedure. Derivatization is based on silylation with N-Methyl-N-trimethylsilyl-trifluoroacetamide (MSTFA) during the step of thermal desorption. The high temperature of 300 °C during desorption is utilized for the in-situ derivatization on the collection substrate (quartz fibre filters) accelerating the reaction rate. Thereby, the analysis time is as short as without derivatization. At first the filter surface is dampened with derivatization reagent before insertion of the sample into the thermal desorption unit. To ensure ongoing derivatization during thermal desorption the carrier gas is enriched with MSTFA until the desorption procedure is finished. The precisions of all studied analytes were below 17 % within a calibration range from 22 pg (abietic acid) up to 342 ng (levoglucosan). Limits of quantification (LOQ) for polycyclic aromatic hydrocarbons (PAH) were between 1 pg (fluoranthene) and 8 pg (indeno[1,2,3-cd]pyrene), for resin acids 37–102 pg and for studied phenols 4–144 pg. LOQ for levoglucosan was 17 pg.