An 86-year-old man was admitted to our department with complaints of intermittent upper abdominal pain. Ultrasonography of the abdomen showed dilated extrahepatic bile ducts containing stones; however, the gallbladder was not clearly identified. Magnetic resonance cholangiopancreatography showed dilated extrahepatic ducts and choledocholithiasis without gallbladder visualization. The stone extraction was performed with endoscopic sphincterotomy. Three-dimensional images using spiral-computed tomography after intravenous-infusion cholangiography clearly demonstrated an obstruction of the cystic duct. The patient was scheduled for laparoscopic cholecystectomy. At laparoscopy, the gallbladder fossa was not identified on the undersurface of the liver. Despite a thorough examination of the intrahepatic (left-sided within the lesser omentum), retroperitoneal, retrohepatic (within the falciform ligament), retroduodenal, and retropancreatic areas using laparoscopic ultrasonography, the gallbladder was not found. After careful dissection of the hepatoduodenal ligament, the dilated extrahepatic bile duct and a 1-cm length of hypoplastic cystic duct were found. Gallbladder agenesis is usually accompanied by the lack of the cystic duct. The present case is the third report of gallbladder agenesis with a patent or hypoplastic cystic duct.