Circadian regulation is an endogenous self-sustaining mechanism that drives temporal gene expression and, amongst others, affects the diurnal patterns of photosynthesis (A) and stomatal conductance (g(s)). Here we review current knowledge on how circadian regulation drives diurnal gas exchange from genes to ecosystems in the field. Molecular mechanisms underlying the structure of circadian clocks and how they regulate A and g(s), in a few model species are starting to be elucidated but additional data are required to understand regulation across phylogenies, especially within the gymnosperms, and across environments and scales. Circadian rhythms were responsible for 15-25% and for 30-35% of the daytime oscillations in A and g(s) respectively, across the C3 and C4 species for which data are available. Consequently, circadian effects over diurnal gas exchange are of similar magnitude to the effects of temperature or vapor pressure deficit. Moreover, recent findings indicate how circadian rhythms could exert significant impacts on ecosystem patterns of gas exchange, which would challenge conventional approaches to derive the environmental flux dependences. Progress in transferring laboratory findings to the field is being hampered by lack of suitable experimental and modeling facilities that can disentangle circadian effects from environmental responses in the field and in ecosystems, and methodological recommendations are offered. The effects of environmental stressors on circadian regulation of gas exchange are also poorly understood. We document how circadian control of gas exchange may be adaptive by allowing plants to anticipate highly predictable environmental cues, but also by increasing the diversity of potential gas exchange responses to environmental variation in plant populations.