High performance liquid chromatography (HPLC) with phenylisothiocyanate (PITC) is recently used for confirming the diagnosis of inborn errors of metabolism (IEM) especially amino acid disorders in Malaysian children. The method of HPLC used is a precolumn derivatization of amino acids with phenylisothiocyanate and is separated by reversed phase chromatography using 3.9 x 300 mm free amino acid columns and is detected by a UV/Vis detector. The samples are obtained from cases suspected of inborn errors of metabolism, especially of amino acid disorders, which are detected clinically by pediatricians. Initially, samples from patients suspected of inborn errors of metabolism, either urine or serum, are run on one-dimensional thin layer chromatography and supplementary chemical tests to detect the abnormal bands and associated abnormalities respectively. Positive samples are further run on HPLC to determine the specific amino acids abnormality. An examples of a case of maple syrup urine disease is discussed, based on the thin layer chromatography findings and HPLC findings.