Objective　To learn the incidence of the inherited metabolic diseases in Beijing. Methods Urine samples were analyzed by gas chromatography-mass spectrometry??GC-MS??for inherited metabolic diseases in high risky infants in Beijing . Results Urine samples from 411 high risky infants were analyzed by gas chromatography-mass spectrometry. 269 cases (65.5%) were detected to have metabolic abnormalities, including 19 cases (4.6%) diagnosed of inherited metabolic diseases in which there were 15 cases of methylmalonic academia and 1 case each of propionic academia, hyperphenylalaninemia, urea cycle abnormality and pyroglutamic aciduria. There were 22 suspected cases (5.4%) of inherited metabolic diseases including 13 cases of lactic acidosis, 5 cases of primary glycerol aciduria, 4 cases of fatty acid metabolic disorders including 1 case each of Citrin defects, tyrosinemia, galactosemia 3-methylcrotonoyl coenzyme A carboxylase deficiency and maple syrup urine disease. There were also 228 cases (55.5%) of metabolic abnormalities, such as increasing urine levels of lactic acid, sucrose,lactose, galactose, N-acetyl tyrosine, succinic acid, dicarboxylic acid and abnormal serine/threonine ratio. Conclusions Methylmalonic academia might be the most common inherited metabolic diseases in high risky infants in Beijing. For infants with clinical manifestations but unclear etiology, GC-MS should be performed. MS-MS and gene analysis could be combined if necessary.