The circadian clock is a 24 hour timing device that co-ordinates biological activity with day/night cycles. The long history of systems analysis of circadian biology extends back to the first half of the last century when theoretical studies based on physiological experiments predicted the essential network properties, architecture and performance of circadian oscillators long before the first genetic components were isolated in the second half of the century. Systems approaches have continued to be important in analysing the circadian network in the model plant Arabidopsis thaliana and in mammals. We describe how systems analyses of transcriptional changes have led to formal mathematical models of circadian oscillators. Predictions within these mathematical models have been used to identify potential new components of circadian systems. Cross-referencing circadian regulation of transcript abundance with transcriptomic responses to abiotic and biotic signals has increased understanding of the nature of circadian clocks and their significance in regulating the daily life of plants and animals. We also highlight the need for systems analyses of the circadian regulation of proteins, metabolites and other physiological activities such as ion channel regulation.