Sleep-related respiratory dysfunction compromises the health and quality of life of millions of people worldwide, underscoring the need for a full understanding of the mechanisms by which the respiratory control system is altered at night. This paper suggests the hypothesis that the circadian timing system may play a role in the pathogenesis of some types of sleep-related breathing disorders. Recent studies have provided evidence that the circadian timing system has an influence on respiration and respiratory control, even in the absence of sleep. These new data are reviewed and potential mechanisms underlying the circadian modulation of breathing are outlined, identifying important gaps in our knowledge. It is proposed that circadian rhythms in respiratory control may increase the propensity for nocturnal respiratory instability and recurrent apnea. Importantly, circadian and sleep mechanisms appear to have additive effects on breathing, suggesting that the circadian timing system can potentially amplify or suppress sleep-related breathing abnormalities, depending upon the characteristics of the circadian output and the time of day at which sleep occurs.