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Background: Encephalopathy of different etiologies in infants is often the reason for central respiratory insufficiency which eventually leads patients to the Pediatric Intensive Care Unit. Magnetic resonance imaging (MRI) and brainstem auditory evoked potentials (BAEPs) may be useful to identify brainstem alterations among patients with respiratory insufficiency of central origin. MRI is a compulsory technique to identify brain abnormalities, but may fail to detect brainstem lesions of small dimensions. BAEPs play a highly sensitive role on brainstem dysfunction identification because of the generators of different peaks which are related to specific brainstem structures., Methods: The study included ten infants affected by encephalopathy of different etiologies and early neurological respiratory failure. To evaluate BAEPs, the surface electrodes were placed at the vertex (Cz) and on each mastoid side., Results: All subjects presented alteration of BAEPs. The brain MRI revealed selective injury of the brainstem in four patients and supratentorial alterations in six patients., Conclusions: The early identification of brainstem lesions in mechanically ventilated infants with encephalopathy may reduce the weaning off mechanical ventilation's attempt numbers and provide early informative discussions with families and clinical caregivers about treatment options, such as tracheostomy, long term ventilation and the reduction of their length of PICU stay. Furthermore, this would support the evaluation process concerning the affected children, their families and the needs of other social groups, including health systems.