Congenital malformation of the gallbladder and cystic duct that cause operative difficulty are rare developmental abnormalities of embryogenesis. We report the case of a 47-year-old male patient who presented with right upper quadrant pain, tenderness, mild jaundice, moderately elevated liver function tests, and ultrasound evidence of acute calculus cholecystitis. Magnetic resonance cholangiopancreatography (MRCP) excluded choledocholithiasis, but revealed the cystic duct anomaly. A difficult laparoscopic cholecystectomy was performed successfully. This is an unusual case of laparoscopic cholecystectomy for severe acute calculus cholecystitis in a patient with very low conjunction to the common bile duct (CBD) of a long, parallel cystic duct.