OBJECTIVE: Many inborn errors of metabolism have similar presenting clinical manifestations, making early diagnosis difficult. We report our experience with tandem mass spectrometry combined with urine gas chromatography/mass spectrometry as a means of definitively diagnosing inborn errors of metabolism. METHODS: One hundred and thirty-two children with suspected inborn errors of metabolism but without specific clinical manifestations, admitted to the Xinhua Hospital Affiliated to Shanghai Jiaotong University School of Medicine between June 1, 2003 and September 30, 2006, were studied. Children received routine biochemical examinations, as well as mass spectrometry and gas chromatography-mass spectrometry. RESULTS: Fifteen cases (11.5%) were confirmed as having inborn errors of metabolism, including 6 cases of methylmalonic acidemia, 2 of propionic academia, 2 of Type II citrullinemia, 1 of biotinidase deficiency, 1 of tyrosinemia, 1 of maple syrup urine disease, 1 of omithine transcarbamylase deficiency and 1 of very long chain Acyl CoA dehydrogenase deficiency. CONCLUSIONS: The combined use of tandem mass spectrometry with urine gas chromatography mass spectrometry is useful for early diagnosis of inborn errors of metabolism in children with suspected inborn errors of metabolism but without specific clinical manifestations.