The Virtual Comparative map (VCMap) is a visualization tool that allows cross-species comparisons of genomic sequence, genetic, and radiation hybrid map data from human, mouse, rat, cattle, chicken, horse, and pig. The objective of VCMap is to facilitate sharing of annotation across species, including genes, markers and QTL. Users may also view additional private data such as Genome-Wide Association Studies, NextGen sequencing results or any data in BED, BAM, GFF, SAM, VCF or space-delimited text format. The previous version of VCMap (2.0) uses UCSC track 1 conservation data stored in a MySQL database to draw comparative maps dynamically using a Java webstart application. Due to the limitations at UCSC, not all species have detailed homology information and updates occur infrequently. VCMap3.0 uses a redesigned database that facilitates ENSEMBL Compara data to obtain homology information with more species availability and frequent updates. These updates improve cross-species comparisons to complement existing features. Additional upgrades to the system have enhanced the speed of loading large private datasets for visualization. Future development of the tool will allow inclusion of cross-species phenotype ontologies and additional annotations. Our long-range goals are to allow more seamless incorporation of new homology information. To achieve these goals we will develop pipelines to facilitate rapid updates of homology information with new genome builds, add the ability to view additional species, and make a generic species genome comparison tool. The VCMap website is available at http://www.animalgenome.org/bioinfo/projects/vcmap/. This project is supported by the USDA-NRI 2007-04187.