An 84-year-old woman was admitted to the hospital because of pyloric stenosis caused by gastric cancer. Abdominal computed tomography and magnetic resonance imaging failed to demonstrate the gallbladder, but showed a gallstone in a duct-like structure parallel to the common bile duct. When laparotomy was performed, the gallbladder and the fossa were not observed, and a blind-end duct, similar to a cystic duct, was found beside the common bile duct. Incisional exploration of the common bile duct was done after distal gastrectomy; the gallstone was not found in the common bile duct, but in the duct parallel to it. By observing the duct beneath the common bile duct with a cholangioscope, we considered it to be a hypoplastic cystic duct. After the gallstone was removed, a T-tube was placed into the common bile duct. Agenesis of the gallbladder is a rare congenital anomaly and is often asymptomatic. As far as we know, this is the first report of gallbladder agenesis with a hypoplastic cystic duct impacted with a stone. Careful intraoperative examination using a cholangioscope is useful to confirm the structure of the common bile duct.