Background: Data on acid and non-acid reflux patterns and esophageal function in Japanese patients with non-erosive reflux disease (NERD) are limited. The aim of this study was to use combined multichannel intraluminal impedance pH monitoring (MII-pH) and high-resolution manometry (HRM) to investigate the characteristics of Japanese patients who were treated with a "double-dose" (20 mg) of rabeprazol (a proton-pump inhibitor; PPI) for persistent symptoms of NERD. Methods: Twenty-five patients who complained of typical gastroesophageal reflux disease symptoms, which had occurred more than twice a week despite treatment with rabeprazol, were enrolled in the study. All patients underwent upper endoscopy, esophageal HRM, and 24-h MII-pH monitoring while double-dose PPI therapy was continued. Results: Twelve (48.0%) of the patients had a positive symptom index (SI) with 234 recorded symptoms, 127 (54.3%) of which were related to reflux episodes. Of those with reflux episodes, 29 (22.8%) were related to acid reflux, while 98 (77.2%) were the result of a weaker acidic reflux. In acid reflux and in mixed (liquid-gas) reflux, the proximal esophageal region was involved to a significantly greater degree (P<0.002 and P=0.005, respectively) than the distal region. In liquid reflux, there was no difference between the distal and proximal regions. HRM showed that proximal motility parameters were significantly more defective than in those of healthy volunteers. Conclusions: MII-pH monitoring indicated that weakly acidic reflux and mixed refluxate in the proximal esophagus is the major cause of persistent symptoms in patients with NERD who are being treated with PPI. HRM showed that proximal esophageal dysfunction might be a key condition that facilitates reflux.