Impaired esophageal clearance is important in the pathogenesis of gastroesophageal reflux disease (GERD). It is unknown whether esophageal clearance improves following antireflux surgery. The aim of this study was to investigate the effect of laparoscopic Nissen fundoplication (NF), laparoscopic partial posterior (Toupet) fundoplication (PPF) or medical therapy on esophageal clearance. This was a prospective nonrandomized crossover study. Sixty patients were evaluated with endoscopy, esophageal manometry, radionuclide scanning of esophageal emptying, and assessment of symptoms prior to surgery or medical therapy and 6 months after treatment. In 20 GERD patients with normal esophageal peristalsis an NF was performed, in 20 patients with impaired esophageal peristalsis a PPF was chosen, and 20 patients received proton-pump inhibitor (PPI) treatment. On endoscopy, esophagitis had resolved in all patients after surgery; two patients with medical therapy still had esophagitis. On manometry, a significant improvement of lower esophageal sphincter competence was seen in both surgical groups. LES relaxation was complete after PPF, but incomplete after NF. Esophageal peristalsis did not improve after medical therapy, was significantly improved after PPF, but had worsened after NF. On scintigraphic esophageal emptying for solid meals, there was no improvement after medical therapy but a significant improvement after PPF. A significant deterioration of esophageal emptying was observed after NF. There was a strong correlation between scintigraphic and manometric evaluation of peristalsis preoperatively (r(s) = -0.87, p < 0.05) and postoperatively (r(s) = -0.82, p < 0.05). There was no change in dysphagia after medical therapy and after NF but a significant improvement after PPF. Globus sensation was significantly improved after PPF but did not change after medical therapy or NF. Postprandial bloating and inability to belch were significantly more common after NF than after PPF. Laparoscopic partial posterior (Toupet) fundoplication can restore a preoperatively defective esophageal bolus propagation on scintigraphy with the same antireflux effect as the laparoscopic Nissen fundoplication, but with lower side-effects.