Here, we focus on how endocrine disruptors having estrogen activity can be analysed based on gene expression profiles. First, a comprehensive survey of the assays for detecting estrogen activity including ligand-binding assays, reporter gene assays, ELISA, and cell growth assays gives the current status in the evaluation of endocrine disruptors and the advantages of using DNA microarrays. Second, a database consisting of gene expression data from various cell types in response to various chemicals is needed for profiling the effects of chemicals as well as for clustering the genes for specific outcomes as a result of such effects. A useful interpretation of clustering requires functional annotations of the genes. Third, one promising approach to the functional characterisation of genes is proteomics and when this is combined with DNA microarray data, analyses of signal transduction pathways will be most effective. A number of genes related with estrogen signalling, signalling via receptors, Ras superfamily members, MAPK family members and AP-1 family members for example, are explained as part of a working hypothesis for such characterisations.