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Background: Brain damage and mental retardation in children can be caused by either excess or depletion of certain amino acids. Up to now there is no reliable reference interval for free plasma amino acid in Iranian children. Objectives: The aim of this study was to provide the reference intervals of free plasma amino acid in healthy Iranian children using high performance liquid chromatography (HPLC) as an accurate method. Methods: 133 children referred to Children's Medical Center, Tehran, Iran for the annual checkup entered the study after filling out the informed consent form. Demographic data and blood samples after overnight fasting were collected. Plasma amino acid concentrations were determined by reverse phase HPLC (RP-HPLC) equipped with a fluorescence detector after precolumn derivatization of amino acids with o-phthalaldehyde (OPA). Results: Female children exhibited significantly higher plasma concentrations of taurine and lysine than male children. Other 20 amino acid values were not significantly different between two gender groups. Positive correlation was observed between age and taurine, leucine and lysine. Conclusions: Our data provided reference intervals of free plasma amino acids in healthy Iranian children. We believe our data can be used as a guideline for pediatricians to identify the significantly deviated amino acid values in children with medical issues such as genetic disorders and some acquired illnesses. Our data is also applicable for further investigations in the field of family medicine. [ABSTRACT FROM AUTHOR]