Endogenous circadian rhythms play a key role in regulating plant growth and development, and in allowing plants to respond and adapt to changing environments. To understand how drought regulates upland rice(Oryza sativa L.) IRAT109, we examined the expression levels of circadian clock and drought-responsive genes through real-time PCR. The results revealed that, first, drought reduced the relative expression level and amplitude of peak expression of several morning circadian clock components (such as OsPRRs, OsLHY and OsZTL1), increased the relative expression level and amplitude of some evening circadian clock components (such as OsTOC1, OsGI and OsELF3), but did not influence OsFKF1. Secondly, the relative expression level of most drought-responsive genes was generally increased, except for OsDST, a negative regulator. Lastly, expression rhythms of most drought-responsive genes were disturbed, but not that of OsCIPK12, OsCDPK7 and OsDREB1A. The results indicate that drought stress modulates the expression of circadian clock components and the interplay regulates diurnal oscillations of relative genes.