Rapid progress in functional genomics is yielding unparalleled opportunities for cancer biomarker discovery. Several procedures including data collection, analysis, verification, and visualization are necessary to identify cancer biomarkers from continuously updated microarray data, which are derived from multiple tissue sources using various methods. BioMarker is designed to integrate these procedures in a user-friendly manner, for practical application by cancer researcher and clinicians. From the feedback of clinical and research application, BioMarker is the first effort to provide a system that facilitates all aspects of biomarker discovery from microarray datasets.