Effective sleep analysis is hampered by the lack of automated tools catering to disordered sleep patterns and cumbersome monitoring hardware. In this paper, we apply deep learning on a set of 57 EEG features extracted from a maximum of two EEG channels to accurately differentiate between patients with insomnia or controls with no sleep complaints. We investigated two different approaches to achieve this. The first approach used EEG data from the whole sleep recording irrespective of the sleep stage (stage-independent classification), while the second used only EEG data from insomnia-impacted specific sleep stages (stage-dependent classification). We trained and tested our system using both healthy and disordered sleep collected from 41 controls and 42 primary insomnia patients. When compared with manual assessments, an NREM + REM based classifier had an overall discrimination accuracy of 92% and 86% between two groups using both two and one EEG channels, respectively. These results demonstrate that deep learning can be used to assist in the diagnosis of sleep disorders such as insomnia.