Background: The use of MS/MS for NBS screening has expanded early detection of multiple disorders of amino acids, organic acids & fatty acid oxidation defects from DBS. In countries with high consanguinity rates like Egypt (20-42%), and lack of national NBS for multiple disorders, except for congenital hypothyroidism (CH), a large number of pediatric patients with mental & physical disabilities are referred to CUPH neurology & genetic OP clinics (550/year). The needs for detection of the aetiology of their manifestations require thorough clinical, laboratory & imaging studies. Objective: This pilot study aimed to set reference values for both amino acids and acylcarnitines detectable by MS/MS for Egyptian children ages ranging from 1 to 12 years from both DBS and plasma to enable objective cut –off values for detection of metabolic disorders among suspected cases.Subjects & Methods: 295 infants and children were enrolled in this study divided into 3 groups: group A (ages from 1 to 3 years), group B (ages from 3 to 5 years) and group C (ages from 5 to 12 years) who presented to the pediatric outpatient clinic for minor complaints. Dried blood spots (DBS) and dried plasma spots were collected and extracted into a methanol solution with deuterium- labeled internal standards, derivatized with butanolic- HCL then submitted to MS/MS analysis. Results: Reference values were set between 2.5nd and 97.5th centiles in each group for DBS as well as dried plasma spots. The results showed that the concentration of amino acids and acylcarnitines were significantly higher in dried blood spots in comparison to their values in dried plasma spots. Also, their concentrations showed gradual decrease by age progression when comparing the three studied groups. Conclusion: This is the first study conducted in Egypt to provide preliminary Egyptian reference values for amino acids and Acylcarnitines in DBS and dried plasma spots by MS/MS. There is an implementing need to set reference values for different age groups. These will help to set cut- off values for objective detection of various inborn errors of metabolism for these age groups.