Gaucher's disease is caused by a lack of glucocerebrosidase, and in type 2 various neurological symptoms can occur;however, the detailed pathogenesis of the condition remains undetermined. Here we performed neurophysiological examinations in an 18-month-old girl with Gaucher's disease type 2 to specify the brainstem lesions. Developmental delay occurred from the age of 8 months, and the patient subsequently showed strabismus, loss of head control, failure to thrive and irregular respiration. She was admitted to our hospital at the age of 18 months. A definite diagnosis of Gaucher's disease type 2 was made from the presence of Gaucher cells and reduced glucocerebrosidase activity. Clinically, limited ocular movements, poor facial expression and bulbar palsy indicated disturbances in the nuclei of oculomotor, trochlear, abducent, facial and ambiguous nerves, although magnetic resonance imaging (MRI) failed to visualize any structural changes in the brain including the brainstem. Neurophysiologically, auditory brainstem response and somatosensory evoked potential demonstrated lesions in the cochlear nucleus and medial lemniscus, respectively. On polysomnography, disturbed sleep parameters during rapid eye movement sleep, in addition to the lack of modification of respiratory patterns by sleep stage, suggested dysfunctions in the locus ceruleus, raphe nuclei and pontine reticular formations. It is likely that these neurophysiological tests can be useful to identify functional lesions that are not detectable by MRI, and should help exploit new treatments for child-onset neurodegenerative disorders such as Gaucher's disease.