Choledochal cyst perforation associated with bacteria is very rare. An 11-month-old infant was admitted to hospital because of fever and bloody diarrhea. Abdominal ultrasonogram revealed a choledochal cyst. Despite antibiotic treatment with initial improvement, jaundice and abdominal tenderness developed 6 days later. Ultrasonography-guided aspiration yielded bile-stained ascites. Emergency operation confirmed the diagnosis of choledochal cyst with perforation. Blood, stool, and bile juice cultures all yielded Salmonella typhimurium. To our knowledge, it is rare that a child with choledochal cyst has systemic infection with S. typhimurium and cyst perforation. We propose that systemic Salmonella infection carries a risk of cyst perforation in patients with congenital choledochal cyst. [J Formos Med Assoc 2007;106(3 Suppl):S20-S23]