Carbohydrates are often referred to as the third molecular chain of life, and they represent the most important post-genomics research targets. Recent reports of their biological functions in signal transduction and cellular recognition have made them promising pharmaceutical targets and disease markers. Like nucleic acids and proteins, the three-dimensional (3D) structures of carbohydrates are important for their molecular functions. Currently, the most abundant source of biological carbohydrate structures is the Protein Data Bank (PDB). As its name indicates, the PDB is a protein structure database. However, carbohydrate structures have often been determined in complexes with protein molecules, as enzyme substrates, lectin ligands, or post-translational modifications. As of Jul 2006, the PDB contained 6,421 carbohydrate-protein complex structures, and the number is increasing rapidly. In this review, the current status of the PDB as the carbohydrate structure database, and the features of several databases derived from the PDB will be summarized. We will also introduce an overview of the bioinformatics tools currently available for analyses of carbohydrate 3D structures.