In the emerging field of metabolomics, there is an increasing need for improving sample derivatization reactions for gas chromatographic-mass spectral analysis of metabolites with large numbers of samples. This protocol details the safe direct derivatization of organic acids using diazomethane in a 96-sample format. Diazomethane is a highly reactive gas that readily forms methyl esters with carboxylic functionalities, with minimal side products or nonvolatile reaction residues. However, diazomethane's reactivity and explosive potential make it hazardous to store and work with. In this procedure, diazomethane is generated in situ and used concurrently to methylate up to 96 samples simultaneously, thus reducing concerns about reagent stability and obviating the need for storage of solutions of the highly reactive gas. Once the diazomethane generator has been assembled, processing 96 samples takes 2-3 h using this procedure.