MOTIVATION: Genome-scale reconstructions and models, as collections of genomic and metabolic information, provide a useful means to compare organisms. Comparison requires that models are similarly notated to pair shared components. RESULT: Matching and comparison of genome-scale reconstructions and models are facilitated by modelBorgifier. It reconciles models in light of different annotation schemes, allowing diverse models to become useful for synchronous investigation.Availability and implementation: The modelBorgifier toolbox is freely available at http://www.brain-biotech.de/downloads/modelBorgifier.zip. CONTACT: jrb [at] brain-biotech.de SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.