We investigated the brainstem integrity in children with primary nocturnal enuresis (PNE) using auditory brainstem responses (ABR), blink reflex and exteroceptive suppression of the masseter muscle. We examined 23 children with PNE (16 male, 7 female; mean age: 10.4 years) and 19 control subjects (11 male, 8 female; mean age: 11.8 years). ABR parameters such as wave latencies, amplitudes and interpeak latencies and blink reflex parameters such as R1 and R2 amplitude and latencies were not significantly different between the 2 groups. Although S2 parameters of the exteroceptive suppression of the masseter muscle were easily and completely obtained from the control subjects, in the PNE group S2 onset latency and duration were not recorded in 26% of the study children (n = 6) (P = 0.01). S2 duration time was significantly lowered in the enuretic group (left side: P = 0.001 and right side: P = 0.003). S2 duration time changes in the enuretic group supports a possible brainstem dysfunction in children with PNE.