In animals, the biological circadian clock generates rhythms with a period of ~24 hours that synchronize to the ambient daily light-dark cycles. Genetic feedback loops in single cells are the primary generator of these rhythms, but they are also observable at the tissue and organ level, as well as in behavior. Thousands of genes in many cell types exhibit circadian rhythms in their expression: this is the clock output. Central questions include which cellular processes are affected by circadian gene expression, as well as whether there are underlying principles for circadian control of cellular pathways. We will give examples from our research activities in the study of the clock output in cells from various tissues in mice with focus on mRNA expression and statistics to investigate clock-controlled processes. We also discuss changes in circadian gene expression due to aging, their consequences and how to detect them. We will further give an example of how mathematical analysis helped us uncover some principles for circadian orchestration of metabolic pathways.