The capture of pathogen gene expression signatures directly from the host niche promises to fuel our understanding of the highly complex nature of microbial virulence. However, obtaining and interpreting biological information from infected tissues presents multiple experimental and intellectual challenges, from difficulties in extracting pathogen RNA and appropriate choice of experimental design, to interpretation of the resulting infection transcriptome, itself a product of responses to multiple host-derived cues. The recent publication of several host-infecting fungal transcriptomes offers new opportunities to study the commonalities of animal and plant pathogeneses, which in turn might direct the rational design of new and broader spectrum antifungal agents. Here, we examine the transcriptional basis of modelled Aspergillus fumigatus, Candida albicans, Cryptococcus neoformans, Ustilago maydis and Magneporthe infections, placing our analysis of the published findings within the context of the various modelling procedures used, and the relevant pathogen lifestyles, to facilitate the first cross-species comparison of fungal transcription during infectious growth. Significant concordance was identified among infecting transcriptomes of the inhaled fungal pathogens C. neoformans and A. fumigatus. The significance of gene clustering and subtelomeric gene repertoires is also discussed.