The analysis of amino acid levels is crucial for neuroscience studies because of the roles of these molecules as neurotransmitters and their influence on behavior. The present study describes the distribution and levels of 16 amino acids (alanine, asparagine, aspartic acid, cysteine, glycine, glutamic acid, isoleucine, leucine, lysine, methionine, phenylalanine, proline, sarcosine, serine, valine, and threonine) in brain tissues (prefrontal cortex, striatum, hippocampus and cerebellum) and the serum. Neurochemical analysis was performed on Wistar rats and C57BL/6 mice using an efficient method for extraction, a fast microwave-assisted derivatization and gas chromatography-mass spectrometry analysis. The amino acid concentration varied across brain regions for 14 of the 16 analyzed molecules, with detection limits ranging from 0.02±0.005μmolL(-1) to 7.07±0.05μmolL(-1). In rats, the concentrations of alanine, glycine, methionine, serine and threonine were higher in prefrontal cortex than in other areas, whereas in mice, the concentrations of glutamic acid, leucine and proline were highest in the hippocampus. In conclusion, this study provides a cerebral profile of amino acids in brain regions and the serum of rats and mice.