Microarray technology is a powerful high-throughput tool for the analysis of host-pathogen interactions that permits simultaneous interrogation of the transcriptional status of thousands of genes. Emerging topics from microarray-based studies employing diverse pathogens and cell types suggest an initial common host response largely characterised by features of the innate immune response. However, specific host gene expression patterns that reflect differences between bacteria of related genera, different species of a particular genus, as well as strains within a single species can also be discerned. These differences are indicative of virulence determinant functions and suggest adaptive survival strategies. These studies have led to a more comprehensive understanding of the host response and identified new avenues of research for potential control strategies against pathogens.