Objective：To detect the inherited metabolic disorders（IMDs） by gas chromatography-mass spectrometry（GC-MS） and to preliminarily investigate the prevalence of IMDs in Chongqing. Methods：A total of 3 377 patients with suspected IMDs in our hospital from May 2016 to May 2018 were underwent the urine organic acid analysis via GC-MS. According to the detecting results and combining with patients’ clinical manifestation，liquid chromatography tandem mass spectrometry（LC-MS/MS） and gene analysis to diagnose the disease；patients’ onset age was obtained by looking through medical history or telephoning their parents. Results：There were 69 patients diagnosed as positive and 20 kinds of IMDs，with a positive detection rate of 2.04%. Among all disorders，there were 30 patients with aminoacidopathy，with the most common one of neonatal intrahepatic cholestasis caused by citrin defi－ciency（NICCD）（17，56.7%） and followed by ornithine tran－scarbamylase deficiency（OTCD）（9，30%）. There were 26 pa－tients with organic acidemias，with the most common one of methylmalonic acidemia（MMA）（13，46.4%），followed by glutaric acidemia type Ⅰ（GA-Ⅰ）（4，14.3%） and propionic acidemia（PA）（3，10.7%）. There were 11 patients with fatty acid metabolic disease，with the most common one of multiple acyl-CoA dehydro－genase deficiency（MADD）（4，36.4%）. Among the six common disorders，40 patients’ onset age was more than one month，except seven patients with MMA，one patient with NICCD，one patient with GA-I and patient with PA. Conclusion：IMDs are not rare，and NICCD，OTCD，MMA，GA-I，PA and MADD are the common disorders in Chongqing，which occurs more frequently in the late neonatal period.