Tetrahymena thermophila is a model eukaryotic organism. Functional genomic analyses in Tetrahymena present rich opportunities to address fundamental questions of cell and molecular biology. The Tetrahymena Gene Expression Database (TGED; available at http://tged.ihb.ac.cn) is the first expression database of a ciliated protozoan. It covers three major physiological and developmental states: growth, starvation, and conjugation, and can be accessed through a user-friendly web interface. The gene expression profiles and candidate co-expressed genes for each gene can be retrieved using Gene ID or Gene description searches. Descriptions of standardized methods of sample preparation and the opportunity to add new Tetrahymena microarray data will be of great interest to the Tetrahymena research community. TGED is intended to be a resource for all members of the scientific research community who are interested in Tetrahymena and other ciliates.