Non-rapid eye movement (NREM) sleep contains periods of arousal instability (cyclic alternating pattern or CAP) and periods of arousal stability (non-CAP). During CAP, arousal oscillates between higher (phase A) and lower (phase B) levels of activation. We evaluated the relationship between CAP and the occurrence of epileptic events, i.e. clinical seizures and generalized interictal discharges, during sleep in 10 patients with Lennox-Gastaut syndrome (LGS). The macro- and microstructure of sleep of 10 attended overnight polysomnograms were analyzed. Compared with 10 age- and gender-matched controls, patients with LGS had significantly less stage 2 and REM sleep and higher amounts of CAP rate (68% vs. 33%; P<0.0001). The number of generalized polyspike bursts per hour of sleep was highest in slow wave sleep (226.5+/-57.6) and lowest in REM sleep (3.9+/-1.5). The polyspike burst frequency was significantly greater (P<0.017) during CAP (213.2+/-60.1) than during non-CAP (100.3+/-40), and within CAP, generalized polyspikes occurred more often (P=0.005) during phase A (461.1+/-127.2) than during phase B (6.1+/-1.9). The total amount of generalized polyspike bursts identified in NREM sleep correlated positively both with the number of A phases containing at least one generalized polyspike (P=0.005) and with the mean number of polyspikes within each of these A phases (P<0.0001). Nocturnal clinical seizures occurred in 8 of the 10 patients and showed a similar trend. We conclude from our results that CAP modulates the occurrence of both clinical seizures and generalized epileptic discharges in LGS by means of a gate-control mechanism: an independent spike generator is inhibited in phase B and non-CAP and bursts with its intrinsic activity in phase A.