We introduce the GeWare data warehouse system for microarray-based gene expression analysis. GeWare centrally stores expression data together with a variety of annotations to support different analysis forms. Compared to previous work, our approach is unique in several aspects. First, GeWare offers high flexibility with a multidimensional data model where expression data is stored in several fact tables which are associated with multiple hierarchical dimensions holding describing annotations on genes, samples, experiments, and processing methods. Second, all annotations are integrated and managed in a generic way, thus supporting easy evolution and extensibility. Especially, consistent experiment annotation is achieved by means of pre-defined annotation templates and controlled vocabularies. Finally, various analysis methods have been integrated using a flexible framework based on the exchange of experiment groups, gene groups and expression matrices. The system is fully operational and has been employed in several research projects.