The circadian clock governs the daily rhythms present in most biological processes, including hormonal signalling and metabolism. The core molecular mechanism of the circadian clock is a transcription-translation feedback loop that governs rhythmic transcriptional activity of the CLOCK/BMAL transcription factors on circadian E-box enhancer elements. We generated a transgenic luciferase reporter line based on concatemerized E-box elements (4xE-box:luc line). This line can trace the maturation of the circadian clock feedback loop activity during development and can be used to map core clock loop activity throughout the zebrafish brain. Furthermore, it can detect the effect of compounds on period length with high sensitivity (lengthening of the period of only 0.7 hours can be resolved).