Purpose: Our aim was the longitudinal assessment of cyst size in fetuses with biliary cystic malformation (BCM) to explore its etiology and the possibility of antenatal differentiation between biliary atresia (BA) and congenital biliary dilatation (CBD). Methods: We conducted a retrospective review of all patients diagnosed antenatally with BCM from 1994 to 2014 at our institutions. Results: The study cohort comprised of three patients with BA and six with CBD. There were no significant differences in the gestational age and cyst size at the first detection of BCM between the two groups. In fetuses with CBD, the cyst size steadily increased as the gestational age advanced, while it fluctuated around 1.5 cm and remained below 2.1 cm in those with BA. However, the ratio of cystic area to fetal trunk area was approximately constant due to linear fetal growth in fetuses with CBD. Conclusion Fetuses with BCM <2.1 cm in the late gestation period were more likely to have BA than CBD. Our observation of cyst enlargement with advancing gestational age in the CBD group was attributed solely to fetal growth. Biliary dilatation in fetuses with CBD and BA might be completed at the onset of BCM.