The Gene Expression Profile Analysis Suite (GEPAS) has been running for more than four years. During this time it has evolved to keep pace with the new interests and trends in the still changing world of microarray data analysis. GEPAS has been designed to provide an intuitive although powerful web- based interface that offers diverse analysis options from the early step of preprocessing ( normalization of Affymetrix and two- colour microarray experiments and other preprocessing options), to the final step of the functional annotation of the experiment ( using Gene Ontology, pathways, PubMed abstracts etc.), and include different possibilities for clustering, gene selection, class prediction and arraycomparative genomic hybridization management. GEPAS is extensively used by researchers of many countries and its records indicate an average usage rate of 400 experiments per day. The web- based pipeline for microarray gene expression data, GEPAS, is available at http://www.gepas.org.