Nerve, muscle and inflammatory cells involved in gastrointestinal (GI) function have high-energy requirements, and are affected in mitochondrial disorders. Familial aggregation of irritable bowel syndrome (IBS) frequently involves mothers and their children. Since mitochondrial DNA (mtDNA) is maternally inherited, mtDNA single nucleotide polymorphisms (SNPs) could confer risk to the development of IBS. The mtDNA SNPs, 16519C>T and 3010G>A, are associated with migraine and childhood cyclic vomiting syndrome. Our hypothesis is that these mtDNA SNPs are associated with functional GI disorders (FGIDs) and GI functions. The mt genome was first tested for the 7028C polymorphism (defining haplogroup H) in 699 patients or controls, and those with 7028C further genotyped at 16519 and 3010. Phenotypes were based on symptoms (validated questionnaires and criteria) and GI physiology using validated motor and sensory studies. IBS-C and IBS-Alt are less prevalent in individuals with the 7028C mtDNA polymorphism than in individuals with 7028T. Conversely, 7028C is associated with higher maximum tolerated volume (lower satiation) compared to 7028T. Among those with 7028C, non-specific abdominal pain (chronic abdominal pain or dyspepsia) was significantly associated with 3010A compared to 3010G (odds ratio 3.3, p=0.02), and slower gastric emptying was statistically associated with 3010G. There were no significant associations of mtDNA genotypes tested and stomach volumes, small bowel or colonic transit, rectal compliance, motor or sensory functions. Thus, variation in mtDNA may be associated with satiation, gastric emptying and possibly pain; further studies of mtDNA in appetite regulation and larger numbers of patients with FGIDs are warranted.