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.