BACKGROUND: The purpose of the study was to assess the efficacy of laparoscopic-assisted removal of protein plugs from the common channel in choledochal cysts. METHODS: Between 2001 and 2009, 34 patients with choledochal cysts (mean age, 4.98 years) with protein plugs in the common channel successfully underwent laparoscopic cyst excision and Roux-en-Y hepatojejunostomy. Under direct vision during laparoscopy, urethroscopes or catheters were inserted into the common channel to irrigate and remove the protein plugs. Complete clearance was confirmed by either direct urethroscopic visualization or cholangiogram that demonstrated (1) no filling defects in the common channel, (2) significant reduction of common channel diameter, (3) free passage of contrast agent into the duodenum, and (4) no pancreatic duct reflux. Operative time and blood loss, postoperative hospital stay, duration of drainage, postoperative complications, perioperative ultrasonographic findings, and laboratory results were reviewed.