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The rapid progression of farm animal genomics has introduced novel technologies capable of presenting global descriptions of biological systems at the level of gene and protein expression and protein interaction. To fully benefit from these developments, experimental designs have to be adapted to these new technologies, and important considerations must be made in the choice of technologies and methods of analysis to be used. This paper addresses practical issues in the use of microarray based methods for gene-expression analysis in farm animals, and provides an overview of different array-platforms as well as a presentation of methods and software for the analysis of array data. Experimental design and the selection of animals and samples for microarray studies in farm animals present novel challenges, which are often overlooked. In particular, the frequent use of half sibs and full sibs in animal studies increases the risk of falsely identifying genes as being differentially expressed, due to genetic linkage of the gene to a QTL or a major gene affecting the trait in question.