To investigate the effects of a short-term feeding stimulus on the expression of circadian genes in peripheral tissues, we examined the effects of a 30-min feeding stimulus on the rapid responses and circadian phases of five clock genes (Bmal1, Cry1, Per1, Per2 and Per3) and a clock-controlled gene (Dbp) in the heart and kidney of rats. A 30 min feeding stimulus was sufficient to alter the transcript levels and circadian phases of peripheral clock genes in a tissue-specific manner. The transcript levels of most clock genes (Bmal1, Cry1, Per1, and Per2) were significantly down-regulated in the heart within 2 h, which were affected marginally in the kidney (except Per1). In addition to the rapid response of clock gene expression, we found that the circadian phases of these clock genes were markedly shifted by the 30-min feeding stimulus in the heart within 1 day. However, the same feeding stimulus almost not affected the peak phases of these clock genes in the kidney. Moreover, these differential responses of peripheral clocks to the 30-min feeding were also similarly reflected in the expression of circadian output gene Dbp. Therefore, a 30-min feeding stimulus was sufficient to induce dyssynchronized peripheral circadian rhythm and might further result in disordered downstream physiological function in rats.