Abstract A method for determining the position and enrichment of isotope labels in amino acids using gas chromatography/mass spectrometry is described. [α- 15N]- and [ϵ- 15N]lysine, [1- 13C]- and [ 15N]alanine and -leucine, and [1- 13C]-, [2- 13C]-, [3- 13C]-, and [4- 13C]aspartic acid were investigated. Standards for each isotope label were prepared and analyzed under scan conditions, and line pairs characteristic for the label were identified. The standards were reanalyzed under selective ion monitoring conditions to verify the vehavior of the line pairs. Mixtures of amino acids containing different isotope labels or the same label in different positions were prepared and analyzed under selective ion monitoring conditions. Enrichments were determined with high precision and relative errors ranging from 0.14 to 36%.