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Background and Aims Magnetic compression anastomosis is a rescue technique for recanalization of complete biliary strictures. Here, we present magnetic compression anastomosis with novel through-the-scope magnets in patients with complete duct-to-duct anastomosis obstruction after liver transplantation. Methods The magnets were 2 and 2.4 mm in diameter, with a hole at the center for inserting a guidewire. One of the magnets was advanced through the scope up to the distal site of the stricture by using a 7F pusher. The other magnet was pushed percutaneously through the 10F sheath. The procedure was terminated when the magnets were approximated or properly aligned. Recanalization was followed by percutaneous cholangiography. Patients underwent multiple plastic stenting after recanalization was achieved. Results Nine patients with a stricture length of less than 1 cm, a stump in the donor bile ducts close to the stricture, and proper positioning of the bile duct stumps, underwent magnetic compression anastomosis. Seven patients had a live donor–related liver transplantation. The mean stricture time was 24.1 ± 17.1 months. The mean stricture length was 4.0 ± 1.2 mm. Recanalization was achieved in 7 patients (77%) after a mean recanalization time of 8.1 ± 4.7 days. There was no recurrence after 4.8 ± 3.8 months of stent-free follow-up. No adverse events were observed. Conclusions The through-the-scope magnet procedure was effective in the recanalization of complete anastomotic biliary obstructions after liver transplantation in a selected group of patients with a short stricture length and an appropriate anatomy.