This paper presents an initial description of the BindingDB, a public web-accessible database of measured binding affinities for various molecular types (http://www.bindingdb.org). The BindingDB allows queries based upon a range of criteria, including chemical similarity or substructure, sequence homology, numerical criteria (e.g. DeltaGo < 5 kcal / mol) and reactant names (e.g. “lysozyme”). Principles of Human-Computer Interactions are being employed in creating the query interface and user-feedback is being solicited. The data specification includes significant experimental detail. A full dictionary has been created for isothermal titration calorimetry data in consultation with experimentalists and data dictionaries for enzyme-inhibition and other measurement techniques are being developed. Currently, the BindingDB contains several data sets of broad interest, such as antigen-antibody binding and cyclodextrin / small-molecule binding. However, it is anticipated that online deposition by experimentalists will ultimately contribute a larger flow of data. We are actively developing software and file specifications to facilitate such deposition.