Circadian rhythms are physiological and behavioral cycles with a period of approximately 24 hours that are generated by an endogenous clock, or oscillator. Found in diverse organisms, they are precisely controlled and provide growth and fitness benefits. Numerous microarray studies examining circadian control of gene expression have reported that a substantial fraction of the genomes of many organisms is clock-controlled. Here we show that a long-period mutant in Arabidopsis, rve8-1, has a global alteration in phase of all clock-controlled genes. After several days in constant environmental conditions, at which point the mutant and control plants have very different circadian phases, we found 1557 genes to be differentially expressed in rve8-1, almost all of which are clock-regulated. However, after adjusting for this phase difference, only a handful show overall expression level differences between rve8-1 and wild type. Thus the apparent differential expression is mainly due to the phase difference between these two genotypes. These findings prompted us to examine the effect of phase on gene expression within a single genotype. Using samples of wild-type plants harvested at thirty-minute intervals, we demonstrated that even this small difference in circadian phase significantly influences the results of differential expression analysis. Our study demonstrates the robust influence of the circadian clock on the transcriptome and provides a cautionary note for all biologists performing genome-level expression analysis.