Transcriptomic analysis using quantitative reverse transcriptase polymerase chain reaction (QRT-PCR) facilitates analysis of nuclear and mitochondrial-encoded mitochondrial genes, enabling mechanisms and regulation of signaling pathways to be explored. To illustrate this technique, we use genes of the mitochondrial respiratory chain. We show that several components of the mitochondrial respiratory chain respond to stress, in particular the alternative oxidase. This chapter describes a method involving total ribonucleic acid (RNA) isolation and QRT-PCR for the detection and analysis of transcriptional changes that accompany seven commonly used chemical stresses. This methodology describes an accurate technique to determine quantitatively absolute transcript levels and a platform to facilitate comparison between responses to other stress stimuli.