This work aims to investigate sleep microstructure as expressed by Cyclic Alternating Pattern (CAP), and its possible alterations in pathological sleep. Three groups, of 10 subjects each, are considered: a) normal sleep, b) psychophysiological insomnia, and c) sleep misperception. One night sleep PSG and sleep macro- micro structure annotations were available per subject. The statistical properties and the dynamics of CAP events are in focus. Multiscale and non-linear methods are presented for the analysis of the microstructure event time series, applied for each type of CAP events, and their combination. The results suggest that a) both types of insomnia present CAP differences from normal sleep related to hyperarousal, b) sleep misperception presents more extensive differences from normal, potentially reflecting multiple sleep mechanisms, c) there are differences between the two types of insomnia as regard to the intertwining of events of different subtypes. The analysis constitutes a contribution towards new markers for the quantitative characterization of insomnia, and its subtypes. © 2013 IEEE.