Many microorganisms establish intimate associations with plants. Whether pathogenic or symbiotic, such interactions involve complex recognition events between plant and microorganism, leading to signalling cascades and regulation of countless genes required for, or associated with, the interaction. Here we introduce the concept of the 'interaction transcriptome': the combined components of the transcriptomes of both plant and microorganism that are expressed during the interaction. We discuss how RT-PCR, genomics and bioinformatics approaches are combined to meet the daunting challenge of identifying and characterizing transcriptional changes during infection or symbiosis.