Microarraying is rapidly becoming the method of choice for high throughput gene expression analysis. Using this relatively simple technique of arraying cDNA's or oligos at high density onto glass slides, it is now possible to analyse thousands of genes in a massively parallel manner. Here we describe some of the parameters that have to be optimised in order to achieve good quality, meaningful microarray data. These parameters include various slide substrates, pin design, hybridisation systems and reading of arrayed slides.