Omega (omega)-3 polyunsaturated fatty acids appear to be effective in preventing and treating parenteral nutrition-associated liver disease, and several mechanisms were proposed for this observation. An 8-week-old male infant with cholestasis and acholic stool was diagnosed non-syndromic intrahepatic interlobular bile duct paucity by open-wedge liver biopsy. Initially he was treated with usual supportive medical therapy, including ursodeoxycholic acid. However, the clinical status and laboratory tests did not improve. Omega (omega)-3 polyunsaturated fatty acids (initially intravenous administration and oral administration later), were started and his liver function, including aminotransferase level and bilirubin levels normalized, and the ivory stool color turned green. We report the possible effectiveness of omega-3 polyunsaturated fatty acids as a potent choleretic agent for non-syndromic intrahepatic interlobular bile duct paucity, a very rare structural pediatric hepatic disease.