We used whole genome expression analysis to investigate the changes in the mRNA profile in cells lacking the Saccharomyces cerevisiae RNA polymerase II subunit RPB4 (delta RPB4). Our results indicated that an essentially complete shut down of transcription occurs upon temperature shift of this conditionally lethal mutant—98% of mRNA transcript levels decrease at least two-fold, 96% at least four-fold. This data was supported by in vivo experiments that revealed a rapid, and greater than five-fold decline in steady state poly(A) RNA levels after the temperature shift. Expression of several individual genes, measured by Northern analysis, was also consistent with the whole genome expression profile. Finally, we demonstrated that the loss of RNA polymerase II activity causes secondary effects on RNA polymerase I, but not RNA polymerase III, transcription. The transcription phenotype of the delta RPB4 mutant closely mirrors that of the temperature-sensitive rpb1-1 mutant frequently implemented as a tool to inactivate the RNA polymerase II in vivo. Therefore, the delta RPB4 mutant can be employed to easily design strains that enable the study of distinct post-transcriptional cellular processes in the absence of RNA polymerase II transcription.