MetRxn is a knowledgebase that includes standardized metabolite and reaction descriptions by integrating information from databases and genome-scale metabolic models into a single unified data set. All metabolite entries have matched synonyms, resolved protonation states and are linked to unique structures. All reaction entries are elementally and charge balanced. This is accomplished through the use of a workflow of lexicographic, phonetic, and structural comparison algorithms. MetRxn allows for the download of standardized versions of existing genome-scale metabolic models and the use of metabolic information for the rapid reconstruction of new ones. By conforming to standardized metabolite and reaction descriptions, MetRxn enables users to efficiently perform complex queries and comparisons across models and/or databases. For example, common metabolites and/or reactions between models and databases can rapidly be generated along with connected paths that link source to target metabolites. MetRxn supports export of selected reactions and models in SBML format.