The pathogenesis of megaesophagus in chronic Chagas disease, which is caused by infection with the parasite Trypanosoma cruzi is compelling. Individuals with megaesophagus often present achalasia and disturbances of peristalsis and neuronal loss. Esophageal samples were obtained from 6 T. cruzi infected individuals with megaesophagus, 6 T. cruzi infected individuals without megaesophagus, and 6 noninfected individuals who underwent necropsy procedures. Using one antibody specific for neuronal Nitric Oxide Synthase (nNOS) and another specific for Protein Gene Product 9.5 (PGP-9.5), which is a pan-neuronal marker, we demonstrated the relative area of nitrergic innervation. Additionally, we analysed the area occupied by Interstitial Cells of Cajal (ICCs) with antibody specific anti-CD117. The analyses presented here show that the relative area of nitrergic innervation is reduced in T. cruzi infected individuals with megaesophagus. Furthermore, we demonstrated reduced CD117-immunostained areas in the esophagus of T. cruzi infected individuals. Statistical analyses revealed a positive correlation between the relative area of nitrergic innervation and the density of ICCs in the same infected individuals. Considering data from the literature, we raised the hypothesis that the loss of nitrergic nerve fibers and ICCs could be view as an interdependent phenomenon occurring in the esophagus of T. cruzi infected individuals and that it could contribute to peristalsis disturbances, to achalasia and to megaesophagus development.