In recent years, circadian rhythms are more and more accepted to play a significant role in a number of diseases, based on a growing understanding of their mechanism and relevance for physiology and disease. This progress is depending on measuring clock parameters such as period and phase as well as amplitude. Here, I will focus on what we can learn from pre-clinical models by highlighting two recent projects our group is involved in: (1) A novel tissue-specific circadian reporter mouse model, and (2) developing methods to determine clock status from transcriptomic data making use of the interdependence of clock gene expression.