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The main objective of this study was to evaluate the cost-effectiveness of incorporating Tandem Mass Spectrometry (MS/MS) into the National Neonatal Screening Program in Brazil for the early diagnosis of two Inborn Errors of Metabolism: Phenylketonuria (PKU) and Medium-Chain Acyl-CoA Dehydrogenase Deficiency (MCAD). The dissertation was divided into three sections. The introductory text presents an overview and current status of Inborn Errors of Metabolism, Neonatal Screening, and the diagnostic methodologies for the Inborn Errors of Metabolism screened in question. Next, the justification, objectives, methodological approaches adopted, results, and discussion are presented, along with literature on other economic evaluations that assessed the cost-effectiveness of incorporating Tandem Mass Spectrometry into Newborn Screening programs.