A mucosal impedance measuring system that is capable of direct and accurate impedance measurements of esophageal mucosa includes example multi-channel intraluminal impedance catheters with inflatable and deflatable components for positioning the impedance sensor electrodes in direct contact with the esophageal mucosa on the inside surface of the esophagus. Impedance measurements from multiple locations in the esophagus are processed for indications of mucosal damage that are indicative of damage due to gastrointestinal reflux disease (GERD), non-erosive reflux disease (NERD), and Barrett's esophagus.