The relationship between esophageal motor abnormalities and GERD has been widely studied. The purpose of this study was to identify the prevalence of ineffective esophageal motility (IEM) in patients with GERD. In addition, we also evaluated esophageal acid exposure, acid clearance, and endoscopic esophagitis in GERD patients with IEM. Of 89 patients enrolled in this study, 47 (52.8%) were found to have nonspecific esophageal motility disorder (NEMD). Forty-four of the 47 (93.6%) patients with NEMD met the diagnostic criteria for IEM. The overall incidence of IEM in GERD patients was 49.4%. Patients with IEM had significant increases in upright and recumbent mean fraction of time pH < 4 (6.70% and 4.38%) and mean recumbent esophageal acid clearance (12.45 min/reflux) when compared to those with other motility findings. Seventeen of the 44 (39%) IEM patients did not have endoscopic esophagitis. On the other hand, 26 of the 39 (67%) patients with normal manometry had endoscopic esophagitis. We concluded that not only is the prevalence of IEM high in GERD, but also that IEM patients have more recumbent gastroesophageal reflux and delayed acid clearance. Combined with endoscopic findings, we propose that IEM can be viewed as a specific entity of primary esophageal motility disorder in patients with GERD.