Objectives: To establish a reference range for acylcarnitines (ACs) and amino acids (AAs) concentrations in dried blood spot (DBS) samples of Omani neonates to detect inborn errors of metabolism (IEM), and to evaluate the effect of age and sex on ACs and AAs. Methods: Electrospray-ionization tandem mass spectrometry (+ESI-MS/MS) was used to determine ACs and AAs concentrations in DBS samples collected from 1302 healthy newborns (0–7 days) delivered at Sultan Qaboos University Hospital between August 2008 and May 2009. Results: More than fifty biomarkers that allow diagnosis of various IEMs were measured, their 1st and 99th percentile values determined, and compared with published international data. Our results were comparable with the corresponding figures from Collaborative Laboratory Integrated Report, despite a much smaller sample size. We found that age had a significant effect on most ACs and AAs except decadienoylcarnitin, decenoylcarnitine, adipylcarnitine, palmitoylcarnitine, steatoylcarnitine, tyrosin, phenylalanine, and valine. Sex of the neonate had insignificant effect on most ACs and AAs except free-carnitine, acetylcarnitine, hexanoylcarnitine, octanoylcarnitine, malonylcarnitine, decanoylcarnitine, dodecenoylcarnitine, dodecanoylcarnitine, and tetradecanoylcarnitine. Conclusions: Tandem mass spectrometer is a highly effective tool for high throughput screening of IEM. This study is the first to publish reference intervals for ACs and AAs from DBS samples of Omani newborns. The results may prove to be of significance when determining cut-off values for newborn screening in the near future.