In the post-genomic era, it is necessary to adapt methods for gene expression and functional analyses to more high-throughput levels of processing. mRNA in situ hybridization (ISH) remains a powerful tool for obtaining information regarding a gene's temporal and spatial expression pattern and can therefore be used as a starting point to define the function of a gene or a whole set of genes. We have deconstructed 'traditional' ISH techniques described for a range of organisms and developed protocols for ISH that adapt and integrate a degree of automation to standardized and shortened protocols. We have adapted this technique as a high-throughput means of gene expression analysis on wax-embedded plant tissues and also on whole-mount tissues. We have used wax-embedded wheat grains and Arabidopsis floral meristems and whole-mount Arabidopsis roots as test systems and show that it is capable of highly parallel processing.