ABSTRACTObjectives:Postrepair esophageal dysmotility and gastroesophageal reflux are well‐known consequences in patients with congenital esophageal atresia (EA) with or without distal tracheoesophageal fistula (TEF). The interstitial cells of Cajal (ICC), considered the intestinal pacemaker, are altered in congenital diseases with abnormal peristalsis, but no data are available for EA. Therefore, presence and maturation of ICC was verified in EA‐TEF newborns.Patients and Methods:Fifteen full‐term neonates underwent repair of EA‐TEF. Control specimens were from 10 newborns who died of nonesophageal diseases. Specimens from upper pouch, fistula, proximal, and distal esophagus were processed for hematoxylin and eosin, c‐kit immunohistochemistry for ICC identification, and transmission electron microscopy. Frequency of c‐kit–positive cells was evaluated in 20 fields per slide using a visual score (absent, very low, low, medium, high, very high). Morphocytometry and statistical analysis were also performed.Results:In the proximal normal esophagus, ICC frequency was very high (3 cases), high (5), and medium (2); distally, it was high (4) and medium (6). In EA‐TEF upper pouch, it was high (2) and medium (13); in the fistula, it was medium (5), low (6), very low (3), and absent (1). Morphocytometry confirmed these results. Comparison between pouch and fistula versus proximal and lower esophagus, respectively, showed statistically significant differences. Transmission electron microscopy demonstrated ICC immaturity in EA‐TEF.Conclusions:The significant lower ICC density in EA‐TEF is in favor for the pathogenesis of esophageal dysmotility frequently observed in such patients.