Compared with luciferase which is widely used as a reporter for circadian rhythms in Arabidopsis thaliana, available fluorescent markers are generally too stable to allow circadian oscillations to be measured. However, we have developed a technique to use the nuclear localization of circadian-controlled transcription factors fused to a fluorescent reporter as a means of measuring circadian rhythms. This technique has the advantage of being suitable for analyzing rhythms at the level of individual cells and in living plants.