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Amino acids in rain samples offer important information on their origin and roles in biogeochemical cycling. This paper describes the development and validation of an alternative analytical procedure for amino acids in atmospheric precipitation using gas chromatography coupled with mass spectrometry (GC–MS). The method detection limits (MDLs) of these amino acids ranged from 1.46 ng L−1 (Proline) to 135 ng L−1 (Arginine), which were much lower than previous methods like high-performance liquid chromatography (HPLC) and comparable to those with liquid chromatography-tandem mass spectrometry (LC-MS/MS). None of the target analytes were detected in blank samples, which was attributed to the optimized pretreatment protocol we adopted. We conclude that the GC–MS based technique developed in this study possesses advantage due to low detection limits. We further demonstrate the applicability of this method by analyzing rain samples from the background atmosphere of the Tibetan Plateau (TP). Similar relative abundances of amino acids were found in the TP rains, marine rains and Arctic ice. The correlations between FAAs and water- soluble ions in the Tibetan Plateau rainwaters showed that the FAAs were most likely originated from biomass burning. Given the similarity of snow and rain samples, our method also provides potential for the future analysis of amino acids in glacier ice cores. • A GC–MS analytical method for amino acids in precipitation was performed and optimized. • The developed method was characterized with high sensitivity and selectivity, while low blank value. • This is the first time that free amino acids were determined in the Tibetan Plateau rain. [ABSTRACT FROM AUTHOR]