Under synchronized conditions daily rhythms run in precise phase relationships. Long lasting shift-work disturbs circadian rhythms and causes metabolism dysfunction. As a result of frequent shifts of the light (L):dark (D) cycle the circadian system has to adjust to a new regimen repeatedly, and organism can never achieve complete adjustment of all circadian rhythms. Nuclear receptor PPARα is supposed to be a functional interface between circadian clock and metabolism, and its interconnection with rev-erbα and pdk4 was proven. The aim of this study was to elucidate responsiveness of the circadian system to the LD cycle mimicking the rotating shift-work with 8-h phase delay every second day. Expression of key clock genes and clock controlled metabolic genes rev-erbα, pparα, and pdk4 was analyzed in the liver and heart of rats by real time PCR. Control Wistar rats were exposed to the regular LD cycle 12:12. The second group was exposed to the LD regimen mimicking shift-work with 8-h phase delays during period of 10 weeks. Sampling was performed in 4-h intervals during 24-h cycle. Clock gene expression in the heart and liver of shifted rats was rhythmic and phase delayed by 8-9 h compared to control. Expression of metabolic genes was influenced more in the liver than in the heart. Results indicate that frequent shifts of LD cycle may interfere with control of lipid metabolism.