Over a period of 19 years an antireflux procedure was performed for gastroesophageal reflux in 59 children. Thirty-two patients underwent Nissen fundoplication and 27 children underwent the Boix-Ochoa antireflux procedure. Six patients died between two and 15 months post surgery of unrelated causes. Follow-up period from six months to 18 years was available in 45 (85%) of the surviving patients. This report summarizes the complications and long-term results with the two surgical procedures and their comparisons. The follow-up evaluation included parental interview and physical examination. Upper GI series and pH monitoring were performed only in children with signs and symptoms of recurrent GER or other post-operative complications. At follow-up with a mean period of 8.7 years following Nissen fundoplication, 87.5% showed good results without any residual symptoms. However, the overall complication rate was as high as 50%. Following the Boix-Ochoa antireflux procedure, 17 (81%) children showed excellent results while four children had recurrent GER. This occurred in two neurologically impaired children and two patients following esophageal atresia repair. No other post-operative complications were encountered with the Boix-Ochoa antireflux procedure. In our experience, the Boix-Ochoa antireflux procedure should be the procedure of choice in the surgical treatment of GER in otherwise normal children while the Nissen fundoplication is preferable in neurologically impaired children and in patients with GER following esophageal atresia repair.