Chagasic patients with megaesophagus were submitted to an endoscopy of the upper digestive tract and the samples were collected with special instruments under sterilized conditions. One of the four samples collected was from the stase liquid and the other three samples were collected from fragments of the esophageal mucosa at one, three and five centimeters from the esophageal-stomach transition (Z line). The samples were analyzed by the Microbiology and Pathologic labs for the identification of microorganisms. After that, the results were correlated with the degree of mega esophagus according to Ferreira-Santos. We observed that the incidence of pathogenic microorganism is very high in megaesophagus, with no relation with the degree of dilatation making the surgery for the treatment of this affection potentially contaminated. There was no significant difference concerning the positivity of the culture relating to the degree of esophagus dilatation.