We have developed a personal computer-based system designed for automated metabolic profiling of urinary organic acids by gas chromatography-mass spectrometry (GC/MS) and data interpretation for organic acidemia screening. For the automated profiling, we compiled retention indices, two target ions and their intensity ratio for 126 urinary metabolites. Metabolites above the cut-off values were flagged as abnormal compounds. The data interpretation was based on combination of the flagged metabolites. Diagnostic or index metabolites were categorized into three groups, "AND," "OR" and "NO," and compiled for each disorder to improve the specificity of the diagnosis. Groups "AND" and "OR" comprised essential and optional compounds, respectively, which and both to reach a specific diagnosis. Group "NO" comprised metabolites that must be absent to make a definite diagnosis. We tested this system by analyzing urine specimens from 48 patients previously diagnosed as having organic acidemias. In all cases, the diagnostic metabolites were identified and each correct diagnosis could be found among the possible diseases suggested by the system. Hence, with this simplified automated system, more people will be able to participate extensively in any screening programs using GC/MS.