Microarrays are a high-throughput assay technology that measures the expression levels of thousands of genes in a single experiment. On the other front is the increasing number of species whose genomes are decoded, thanks to the continuously decreasing cost of DNA sequencing. The two technologies together are revolutionizing biological experimentation. A microarray measurement involves a series of steps including DNA/RNA extraction, enzyme digestion, labeling, hybridization, washing, drying and scanning. Skills and experience are indispensable in each step for high quality and reproducible results. Costs of samples, microarrays, chemicals and labor are not insignificant. A better design generates a dataset with less noise, giving rise to a result of higher statistical significance. A particular design can also limit the analysis methods that can be applied to the data. Careful planning of microarray experiments, therefore, can never be overemphasized.