Schistosomiasis is a wide-spread parasitic disease of many tropical and sub-tropical countries. The current central control measure is the use of single drug praziquantel, although the mode of action is not fully realised and the possibility resistance is a concern. The preferred alternative control strategy would involve a target vaccine, which unfortunately hasnt yet been realised. A useful research tool for better understanding the immunological elimination of an active infection is vaccination with live, radiation attenuation parasites. Both of these important research approaches, whether defining the current drug regime or the immunological interactions between the host and parasite, can be better understood through the profiling of the transcriptional status of the parasite. This review will present some of the recent microarray based studies examining the Schistosoma parasite under chemotherapy or immunological stress. Finally some suggestions on how microarray analyses may better help to identify new detoxification or immuno-evasion mechanisms of the parasite and what subsequent functional validations will be needed to support transcriptional findings.