Abstract Understanding the body's internal clock with regard to wakefulness and sleep requires knowing the circadian rhythm and its timing. The circadian rhythm regulates many body functions including sleep, and misalignment leads to the circadian rhythm sleep disorders. Multiple tools have been developed to pinpoint the circadian phase and its relationship to the sleep–wake cycle. Each of these tools for chronobiological assessment and their application are discussed here. Difficulty in sleeping is the principal reason patients present to a sleep specialist. Beyond determining the presence of sleep-disordered breathing, a patient's intrinsic sleep–wake cycle can be extremely challenging to decipher. Multiple factors influence when a patient goes to bed and wakes. Underneath social pressures, eating habits, work schedules, and the homeostatic drive for sleep lies the circadian rhythm and its impact on sleep. The circadian rhythm exerts a strong effect on sleep and wakefulness. To better appreciate a patient's difficulty in falling asleep or staying awake, the sleep physician needs to understand the sleep–wake cycle in the context of the underlying circadian rhythm. To this end, multiple markers of the underlying circadian rhythm and methods for determining the intrinsic, entrained cycle of sleep and wakefulness, have been developed and researched. The major biological circadian phase markers are the core body temperature, dim light melatonin onset, and cortisol. In addition to this, actigraphy, sleep diaries, the social rhythms metric (SRM), and the morningness–eveningness questionnaire (MEQ) have been developed to assess the behavioral manifestations of the circadian rhythm.