<i>Background/Aims:</i> Growth hormone (GH) is preferentially secreted during slow wave sleep and the interactions between human sleep and the somatotropic system are well documented, although only few studies have investigated the sleep EEG in children with GH deficiency (GHD). The aim of this study was to evaluate the sleep structure of children with dysregulation of the GH/insulin-like growth factor axis. <i>Methods:</i> Laboratory polysomnographic sleep recordings were obtained from 10 GHD children and 20 normal healthy age-matched children. The classical sleep parameters were evaluated together with sleep microstructure, by means of the cyclic alternating pattern (CAP), in GHD patients and compared to the control group. <i>Results:</i> GHD children showed a significant decrease in total sleep time, sleep efficiency, movement time and in non-rapid eye movement sleep stage 2. Although some indicators of sleep fragmentation were increased in GHD children, we found a general decrease in EEG arousability represented by a significant global decrease in the CAP rate, involving all CAP A phase subtypes. <i>Conclusions:</i> The analysis of sleep microstructure by means of CAP, in children with GHD, showed a reduction of transient EEG amplitude oscillations. Further studies are needed in order to better clarify whether GH therapy is able to modify sleep microstructure in GHD children, and the relationships between sleep microstructure, hormonal secretion and neurocognitive function in these patients.