For the purposes of insomnia treatment, pharmacotherapy is widely used, despite the possibility for the use of behavioural treatment of insomnia. Thus, the assessment and treatment of patients with insomnia needs further investigation. This work addresses insomnia treatment evaluation and medication side-effect assessment based on continuous physiological signals such as EEG and ECG monitoring and analysis. EEG and ECG measurements regarding drug medication (verum/placebo cases) have been used in a series of experiments, where spectral and non-linear features have been calculated, for assessing a possible distinct behaviour between the verum/placebo condition and furthermore the relation of features to a physiological conditions. Results show that a combination of EEG and ECG based characteristics, both spectral and non-linear, can be used to reveal the differences introduced with insomnia medication treatment, either being improvement in the hyperarousal state, or undesired side effects.