Nocturnal enuresis is a genetically determined maturational disorder of the central nervous system. Lack of arousal and an inhibition deficit of the micturition reflex have been found as the main dysfunctions leading to wetting during sleep. Both are mediated by nuclei in the brainstem. Therefore, evoked potentials (brainstem auditory evoked potential [BAEP], visual evoked potential [VEP], event-related late acoustic-evoked potential [P300]), and the prepulse inhibition (PPI) of the startle reflex were assessed to further evaluate the brainstem deficit compared with cortical function. Thirty-seven children with nocturnal enuresis, aged 8 years to 14 years 8 months (mean age 10y 7mo [SD 1y 10mo]; 27 males, 10 females) were compared with 40 controls (mean age 10y 7mo [SD 1y 6mo]; 17 males, 23 females). Left interpeak latencies I–III and I–V of the BAEP were increased in children with nocturnal enuresis. VEP measures did not differ between patients and controls. However, children with a positive family history of enuresis showed a shorter latency towards N75 and P100 than children without such a family history. P300 and PPI measures did not differ. We conclude that this strongly supports the postulation of a maturational deficit of the brainstem in nocturnal enuretic children. The increased interpeak latencies I–III and I–V of the BAEP support the hypothesis of an arousal deficit mediated by delayed maturation of brainstem function. Differences in VEP latencies might point towards functional cortical differences in children with a family history of nocturnal enuresis.