Urine organic acid analysis is an essential component of the workup of the patient suspected to have an inborn error of metabolism (IEM). Urine contains several hundred different organic acids, which arise from a multitude of different sources including both normal and abnormal metabolism. They may also arise from drugs and drug metabolism or from xenobiotics and dietary supplements. In addition to the diagnosis of inborn errors of metabolism, the identification of organic acids in a urine sample has a wide range of potential applications, including toxicology and poisonings. The method described below extracts the acidic fraction from urine samples, derivatizes the extracted compounds, and identifies intermediate metabolites by GC-MS. The method utilizes electron impact ionization gas chromatography-mass spectrometry (GC-MS) with total ion collection.