The third case of cyclic vomiting syndrome with a large mitochondrial deoxyribonucleic acid rearrangement is described. Multiple neuromuscular anomalies are present that meet the diagnostic criteria for Kearns-Sayre syndrome, as well as severe symmetrical growth retardation. A 3-kilobase mitochondrial deoxyribonucleic acid deletion (nucleotides 10970-14118) was found at 30-40% heteroplasmy in the blood of the child, but not the mother. Although mitochondrial dysfunction and disease-associated mitochondrial deoxyribonucleic acid sequence variants are believed to be present in most cyclic vomiting syndrome cases, these variants are rarely identifiable on "standard" mitochondrial deoxyribonucleic acid testing. However, finding a rearrangement has clinical implications, and standard testing is recommended in those cyclic vomiting syndrome cases with neuromuscular disease and/or growth retardation, whether maternal inheritance is present or not.