The analysis of amino acids by gas chromatography mass spectrometry (GC-MS) after their derivatization with N-(t-butyldimethylsilyl)-N-methyltrifluoroacetamide was investigated as an alternative approach for the determination of free (FAA) and combined amino acids (CAA) in aerosols. This technique showed excellent linearity with r(2) values ranging from 0.9029 to 0.9995 and instrumental limits of detection ranging from 0.3 to 46pg for the different amino acids. The quality of water used for sample extraction was found to be of utmost importance for achieving low blank levels of FAA and CAA. The addition of isopropanol during the extraction of aerosols was also shown to minimize the coextraction of inorganic salts that interfered with the analysis of FAA, Moreover, the ascorbic acid was found to be the most effective reagent for preventing the oxidative destruction of CAA during the hydrolysis process. By the analysis of spiked aerosol samples, the average recoveries determined for FAA and CAA were higher than 60% and the associated relative standard deviation was lower than 10% for the majority of amino acids. The application of the adopted method in background aerosols of the eastern Mediterranean enabled the unambiguous identification and quantification of 20 amino acids. The total concentration of FAA and CAA in aerosols ranged from 13 to 34ngm(-3) and from 29 to 79ngm(-3), respectively. The GC-MS based method is proposed to overcome several analytical difficulties usually encountered with the conventional HPLC-fluoresence technique.