Microarrays are a platform resource that allow the analysis of the entire transcriptome profile of an organism. New advances in the design and production phases make microarrays the perfect tool for parasitology. The mode of action of many drugs employed to treat parasitic diseases are not understood and coupled with rising concerns of drug resistance, all emphasises the importance of research into the interactions drugs have on their target transcriptomes. One particular disease schistosomiasis, relies on a limited number of chemotherapies for treatment and is a prime example of the need for detailed gene expression information while under drug pressure. Recent microarray studies investigating the basic biology of the major species of Schistosoma and their associated microarray platforms, have provided the basis for future drug mode of action/ drug resistance studies. However determining what is a direct gene expression change due to drug treatment is a hurdle that must be addressed both at the level of parasitology and general toxicology. The utilisation of timecourse and/or drug concentration studies, and generic stress inducers, in combination with advanced statistical/bioinformatical methods will allow the separation of direct, indirect and generic gene expression responses. It is hoped that with these approaches the future investigation of complex biological and physiological questions such as drug mode of action or drug resistance in parasitology may be addressed.