Metabolomics can be described as a simultaneous and comprehensive analysis of small molecules in a biological sample. Recent technological and bioinformatics advances have facilitated large-scale metabolomic studies in many areas, including inborn errors of metabolism (IEMs). Despite significant improvements in the diagnosis and treatment of some IEMs, it is still challenging to understand how genetic variation affects disease progression and susceptibility. In addition, a search for new more personalized therapies and a growing demand for tools to monitor the long-term metabolic effects of existing therapies set the stage for metabolomics integration in preclinical and clinical studies. While targeted metabolomics approach is a common practice in biochemical genetics laboratories for biochemical diagnosis and monitoring of IEMs, applications of untargeted metabolomics in the clinical laboratories are still in infancy, facing some challenges. It is however, expected in the future to dramatically change the scope and utility of the clinical laboratory playing a significant role in patient management. This review provides an overview of targeted and global, large-scale metabolomic studies applied to investigate various IEMs. We discuss an existing and prospective clinical applications of metabolomics in IEMs for better diagnosis and deep understanding of complex metabolic perturbations associated with the etiology of inherited metabolic disorders.