Knowledge from traditional neuroanatomical techniques coupled with more recent advances in functional neuroimaging and molecular genetics have led to a better understanding of how structure relates to function of many biological rhythms. In this article we review the current state of knowledge of the functional neuroanatomy of sleep–wake and circadian rhythms and selected infradian rhythms (eg, menstrual and seasonal). We anticipate that progress in our understanding of the molecular biology of sleep and circadian rhythms will lead to the development of novel therapeutic and prophylactic approaches for improved health and quality of life, and for maintaining performance levels during adverse conditions.