BACKGROUND Mass screening using tandem mass spectrometry(MS/MS) was initiated to determine if the incidence of metabolic disorder is sufficiently high to meet the criteria for newborn screening, and whether or not early medical intervention might be beneficial to the patients. METHODS Newborns and children in a high-risk group were screened using MS/MS from April 2001 to March 2004. Blood spots of newborns were collected between 48 and 72 h after birth. The dried blood spots was extracted with 150 microl of methanol, and analyzed by MS/MS. RESULTS From April 2001 to March 2004, 79,179 newborns were screened for organic, amino and fatty acid metabolism disorders, which account for approximately 5.4% of annual births in South Korea. Twenty-eight newborns were diagnosed with one of the metabolic disorders and the collective estimated prevalence amounted to 1 in 2800 with a sensitivity of 97.67%, a specificity of 99.28%, a recall rate of 0.05%, and a positive predictive value of 6.38%. 6795 infants/children at high risk were screened and 20 were confirmed to have metabolic disorders. CONCLUSION The collective total prevalence of 1:2800 in newborns indicates an underestimation of the incidence of metabolic disorders prior to implementing MS/MS screening in South Korea.