The exact cause of choledochal cysts remains unclear, but several theories have been proposed. One widely accepted theory is an abnormal pancreaticobiliary junction, where the pancreatic duct and bile duct join abnormally outside the duodenal wall. This abnormality may lead to reflux of pancreatic enzymes into the bile duct, causing inflammation and cyst formation. Genetic factors may also play a role in the development of these anomalies.