To investigate the prenatal diagnostic value of chromosome microarray analysis (CMA) in fetuses presenting with ultrasound-based biliary tract system (BTS) anomalies. Amniocentesis was performed and CMA was applied in 271 pregnant women carrying fetuses with BTS abnormalities between April 2015 and December 2020. Pregnancy outcomes and fetal prognosis were followed from 1 to 6years. Sixteen cases (5.9%, 16/271) of chromosomal anomalies were detected. The detection rate of chromosomal abnormalities was significantly higher for fetuses with nonisolated BTS anomalies than for those with isolated BTS anomalies (9.0% vs. 0%, p=0.0017). Follow-up results were obtained from 267 fetuses, including 25 cases of termination of pregnancy (9.4%), 237 live births (88.8%), and 5 (1.9%) neonatal demises. The incidence of congenital biliary atresia in the small gallbladder and nonvisualized gallbladder groups was 3.0% (1/33) and 9.5% (7/74), respectively; however, none was detected on postnatal ultrasound reexamination in the gallbladder enlargement or the other BTS groups. An isolated BTS abnormality is not an indication for invasive prenatal chromosomal analysis. When combined with other ultrasonographic abnormalities, prenatal CMA should be provided. When a small or nonvisualized gallbladder is found prenatally, ultrasonography is limited in the differential diagnosis of congenital biliary atresia.