This report describes the novel sampling of bile from the biliary endoscopic intervention for the molecular identification of parasite infection.A 63-year-old Vietnamese man underwent travel health examination in our hospital. Physical examination showed that his height was 159 cm and weight was 41 kg. He had a 15-year history of intermittent abdominal pain and frequent episodes of diarrhea. Laboratory tests revealed raised eosinophil count (23%, normal range [NR] 0-5), absolute eosinophil count (1899/μL, NR 50-350), and levels of serum immunoglobulin E (3770 IU/mL, NR < 100), aspartate transaminase (270 U/L, NR 0-37), alanine transaminase (210 U/L, NR 0-40), and total bilirubin (1.8 mg/dL, NR 0.2-1.4); however, the serum alkaline phosphatase level was normal (65 U/L, NR 28-94) and non-reactive result for serum human insufficiency virus antibody.Magnetic resonance cholangiopancreatography revealed diffuse dilatation of the biliary tree; the common hepatic and pancreatic duct diameters increased to 1.86 cm and 0.61 cm, respectively.Endoscopic retrograde cholangiopancreatography was performed and a 10-Fr model plastic biliary stent was inserted and flushed with 20 cc normal saline; thereafter, the bile was collected and sent for DNA sequencing. Isospora belli (IB) infection was identified by a polymerase chain reaction.Trimethoprim-sulfamethoxazole 800 mg q6h was administered for 1 month. Liver enzyme levels normalized and negative for concentration method of ova study. The patient was doing well and weighed 51 kg at the outpatient clinic visit 3 months later.This bile sampling with molecular identification has not been described in the literature. We believe that an acute IB infection through fecal-oral transmission may progress to chronic infection of the hepatobiliary system, leading to biliary obstruction and jaundice.