The innovation of present drug design focuses on new targets. However, compound efficacy and safety in human metabolism, including toxicity and pharmacokinetic profiles, but not target selection, are the criteria that determine which drug candidates enter the clinic. Systems biology approaches to disease are developed from the idea that disease-perturbed regulatory networks differ from their normal counterparts. Microarray data analyses reveal global changes in gene or protein expression in response to genetic and environmental changes and, accordingly, are well suited to construct the normal, disease-perturbed and drug-affected networks, which are useful for drug discovery in the pharmaceutical industry. The integration of modelling, microarray data and systems biology approaches will allow for a true breakthrough in in silico absorption, distribution, metabolism, excretion and toxicity assessment in drug design. Therefore, drug discovery through systems biology by means of microarray analyses could significantly reduce the time and cost of new drug development.