In the last two decades quantitative electroencephalogram (EEG) analysis has been widely used to investigate the neurophysiological characteristics of insomnia. These studies provided evidence in support of the hypothesis that primary insomnia is associated with hyperarousal of central nervous system and altered sleep homeostasis. However, we have here underlined that these results have intrinsic methodological problems, mainly related to constraints of standard assessment in clinical research. We have proposed that future studies should be performed on larger samples of drug-free patients, using within-subjects designs and longitudinally recording patients adapted to sleep laboratory. All these methodological improvements will allow to partial out the contribution of individual differences, pharmacological influences and first-night effects on EEG frequencies. Moreover, we have discussed the potential relevance of recent findings from basic research concerning local changes during physiological sleep, which could be extended to the study of insomnia. We have suggested that, if normal sleep exhibits specific regional characteristics, also disorders in initiating and maintaining sleep should be characterized by local changes. The extension of this theoretical framework to the study of insomnia could provide new insights on the underlying pathophysiological mechanisms. As a first step toward the integration of knowledge from basic and clinical research focused on local sleep changes, here we showed some preliminary data from sleep onset recordings of patients with paradoxical insomnia. This approach supports the heuristic potential of our proposal, pointing to a local functional impairment in the process of synchronization in insomniac patients compared to normal subjects, the former exhibiting more beta and less delta and sigma power on anterior scalp locations than the latter.