Metabolomics is a study of small molecules in the body and the associated metabolic pathways and is considered to provide a close link between organism's genotype and phenotype. As with other ‘omics’ techniques, metabolomic analysis generates large-scale and complex datasets. Therefore, various data analysis tools are needed to extract biologically relevant information. The data analysis workflows in metabolomics studies are generally complex and involve several steps. In this chapter, we highlight the concept of metabolomics workflow and discuss the data analysis strategies for metabolomics experiments. We also discuss the available tools that can assist in biological interpretation of metabolomics data. We also present an emerging approach of developing genome-scale metabolic models to study cellular metabolism.