A medical system for approximating the esophageal sacs in an infant afflicted with esophageal atresia. The medical device includes an esophageal catheter and a gastric catheter. The distal end of the esophageal catheter, which includes a magnetic tip, is passed through the esophagus to the upper esophageal sac. The distal end of the gastric catheter, which also includes a magnetic tip, is passed through a gastrostomy and into the lower esophageal sac. The magnetic forces created by both magnets results in approximation of the esophageal sacs. Pressure-induced necrosis establishes a passageway between the esophageal sacs. A stent or stent-graft can be deployed within the established passageway to prevent re-synopsis of the esophagus.