Abstract: In the rapidly growing field of stem cell research, there is a need for universal databases and web-based applications that provide a common knowledge base on the characteristics of stem cells, differentiated cells, and tissues by collecting, processing, and making available diverse types of characterization data. The Characterization Tool is such a novel knowledge database that allows the storage of various characteristics of cells, cell lines, and tissues across different species as well as the analysis of associated marker profiles. Its broad ontology-based framework facilitates the integration of characterization data on the morphological, molecular, and functional level acquired in vivo and in vitro including published marker expressions, cross-references to other databases, text descriptions, information on characterization experiments, and image storage. Data input and modification are recorded on the basis of a secure user management. By means of several easy-to-use data mining tools, marker profiles can be searched and analyzed. The Characterization Tool will aid in the establishment of standards for cell characterization, needed, for example, for stem cell isolation, propagation, and differentiation. The Characterization Tool is available at http://characterizationtool.cellnet.org. It currently holds more than 7000 marker expressions for different human embryonic stem cell lines, adult stem cells, and differentiated cells.