Callosal agenesis is a congenital brain anomaly caused by embryonal hypogenesis of the corpus callosum. Concerning the neurological prognosis, epilepsy and motor disturbance are noted in some cases, while many cases are asymptomatic and the prognosis is good. We report a fetus tentatively diagnosed with hydrocephaly on prenatal echo-encephalography, which was performed without adequate explanation to and understanding of the parents. The parents had not expected an abnormality before the screening, and were subsequently not psychologically prepared for the discovery of the congenital brain anomaly on imaging. Moreover, they received no guidance on how to deal with any possible abnormalities. The pregnant mother was referred to our hospital. Prenatal MRI was performed after informed consent was obtained, and the fetus was diagnosed with callosal agenesis. The patient was followed for 5 years, and neurological development was normal. However, the parents have remained anxious while raising the child. Thus, the prenatal diagnosis of callosal agenesis in this case caused unnecessary mental burden to the parents. Here, we report the course of the case, and discuss the way prenatal ultrasonography should be used as a prenatal screening method, and the importance of counseling before the test.