Inborn errors of metabolism (IEM) are a group of diseases whose diagnosis is usually performed by quantification of several metabolites in biological fluids. The aim of this review is to report the role of the laboratory in IEM diagnosis, highlighting the methods available at present and their advantages and limitations. In conclusion, the huge number of recognized IEMs strongly advises the implementation of new high- output technologies in the laboratories devoted to IEM diagnosis. Although these technologies offer a high diagnostic ability, routine analyses are still very important, as well as consideration of several variables involved in biological sample collection and disease expression that may lead to misdiagnosis of IEMs.