Inherited fatty acid oxidation (FAO) disorders represent a relatively new group of inborn errors of metabolism. Although our understanding of the biochemical and molecular bases of these disorders has improved dramatically in recent years, many patients remain undetected or are given other diagnoses, cyclic vomiting syndrome (CVS) being one of them in a few known cases. Medium chain acyl-CoA dehydrogenase deficiency and the late-onset form of glutaric acidemia type II have been anecdotally misdiagnosed as CVS. In addition, short chain acyl-CoA dehydrogenase deficiency (either true defects or polymorphism-related phenotypes) and particularly short-chain 3-hydroxy acyl-CoA dehydrogenase deficiency may present with clinical and biochemical features that closely resemble CVS. However, the collective role played by FAO and probably other metabolic disorders among the causes of CVS in unknown. Guidelines for a diagnostic approach to FAO disorders at the biochemical level are being presented and discussed. Hopefully, a better understanding and an awareness of FAO disorders could improve the diagnostic evaluation of patients with CVS.