Metabolomics is a recently emerging member of the “omics” technologies. It aims at detecting and quantifying all detectable small molecules, the so-called metabolites, present in a biological sample. Because of the lower number of metabolites compared with the number of genes and proteins identified in genomics and proteomics approaches, data of metabolic studies are less complex and may therefore be more informative. Metabolomics may thus significantly contribute to our understanding of disease mechanisms. Autoimmune diseases are of growing clinical relevance, and due to the chronic nature of these diseases successful treatment is often challenging. In the past years, a variety of studies have been published about the metabolome of autoimmune diseases such as Crohn ’ s disease and rheumatoid arthritis. However, our understanding of the role of different metabolites in the pathogenesis of autoimmune diseases is still far from being complete.