Recent advances in genomics open up new avenues in the analysis of complex behaviors such as sleep. In this analysis, the mouse is the model species of choice because it is amenable to high throughput phenotype and genotype analysis. With the use of the mouse model, unprecedented progress in our understanding of sleep physiology and the treatment of sleep disorders is awaited. This review is intended to provide an overview of available methods and techniques for genetic dissection of sleep in mice. Limits and advantages of different approaches are discussed to highlight the necessity for combining methods to avoid erroneous interpretations. The gap between understanding mechanisms of sleep and its functions may be bridged by finding its molecular bases.