The circadian clock organizes biochemical and physiological processes of an organism in a temporal fashion. This temporal organization is crucial to avoid interference of processes that have adverse effects on each other. Thus, disruption of temporal organization can lead to health problems and behavioral disorders related to mood alterations. To alleviate the consequences of a disrupted temporal organization in the body, it is of importance to understand the processes involved in the synchronization of all body clocks and their phase relationship to the environmental day/night cycle at the mechanistic level. This review will focus on internal and external factors affecting synchronization and function of the circadian system and highlight connections to mood-related behavior.