In this virus-focused chapter, we deal primarily with the use of microarrays for expression analysis (the most popular usage) of host and virus systems during infection. We examine aspects related to array platform choice (spotted and oligonucleotide arrays), probe and array design considerations, experimental procedures and data analysis, normalization, processing, and curation. We also provide in-depth examples for the study of viral transcriptome analysis for both spotted long oligonucleotide (coccolithoviruses) and Affymetrix GeneChip (cyanophage) arrays.