A 2-year-old girl with bilateral sensorineural deafness showed pontine hypoplasia as well as a bulging contour of the pontine tegmentum on magnetic resonance imaging (MRI). There were no bilateral responses of brainstem auditory-evoked potentials (BAEPs). The absent late components of blink reflex (BR) indicated brainstem dysfunction. Chromosomal abnormalities and neurodegenerative or neurometabolic disorders, which might have been the cause of the pontine hypoplasia, were ruled out. The authors describe a rare case with pontine hypoplasia combined with sensorineural deafness and absent blink reflex and suggest that the brainstem in this child may become involved in the early gestation period.