Urinary organic acids are used as diagnostic determinants for the elucidation of inborn errors of metabolism (IEMs). Over the past three decades, the gold standard for measuring these analytes in urine has been gas chromatography/ mass spectrometry (GC/MS). Shown here in pediatric patients, a panel of organic acids is extracted from urine, separated and detected using capillary gas chromatography followed by triple-quadrupole tandem mass spectrometry (MS/MS). Organic acid profiles provide important information regarding the urinary excretion of normal and abnormal acids, which is necessary for the accurate diagnosis of many genetically inherited metabolic disorders and the recognition of other metabolic disturbances. A GC/MS/ MS based method for urine organic acids provides superior selectivity, sensitivity, linearity and reproducibility, as compared to traditional GC/MS methods.