The daily gene expression oscillations that underlie mammalian circadian rhythms show striking tissue differences and may involve post-transcriptional regulation. Both aspects remain poorly understood. We have explored the contribution of translation efficiency to temporal gene expression by ribosome profiling in kidney, and contrasted it with liver data available from the same mice. We observed that rhythmic translation of constantly abundant transcripts was markedly organ-specific. Moreover, translation efficiency modulated the timing of protein biosynthesis from rhythmic mRNAs and the expression of core clock components, consistent with organ-specificity in clock parameters and clock output gene repertoires. Our comprehensive datasets provide insights into translational control beyond temporal regulation. Transcriptome-wide, cross-organ differences in translation rate were widespread and resulted in a phenomenon of translational compensation of constitutive mRNA differences between the tissues. The unique resources provided through our study will serve to address fundamental questions of post-transcriptional control and differential gene expression in vivo.