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Children with migraine headaches appear to have a range of sleep disturbances. The aim of the present study was to assess the NREM sleep instability in a population of school-aged individuals affected by migraine without aura (MoA). Thirty-three children with MoA (20 males, 13 females, mean age 10.45 ± 2.06 years) underwent to overnight Polysomnographic (PSG) recordings and Cyclic Alternating Pattern (CAP) analyses accordingly with international criteria. MoA group showed a reduction in sleep duration parameters (TIB, SPT, TST; ≤ 0.001 for all) and in arousal index during REM sleep and an increase in awakenings per hour (AWK/h) vs. Controls (C) ( = 0.008). In particular, MoA children showed a reduced CAP rate% ( ≤ 0.001), CAP rate% in S1 ( ≤ 0.001) and CAP rate% in SWS ( = 0.004) vs. C. Moreover, A phases distribution were characterized by a reduction in slow wave components (total number CAP A1%, CAP A1 index) ( ≤ 0.001) and an increase of fast components representation (total number of CAP A2% and CAP A3%) ( < 0.001) in MoA vs. C. Moreover, MoA children showed an increased A1 and A2 mean duration ( ≤ 0.001). Our findings show a reduction of arousability in MoA group and lower NREM lower sleep instability associated with MoA in children.