With the rapid accumulation of genetic data for a multitude of different species, the availability of intuitive comparative genomic tools becomes an important requirement for the research community. Here we describe a web-based comparative viewer for mapping data, including genetic, physical and cytological maps, that is part of the SGN website (http://sgn.cornell.edu/) but that can also be installed and adapted for other websites. In addition to viewing and comparing different maps stored in the SGN database, the viewer allows users to upload their own maps and compare them to other maps in the system. The viewer is implemented in object oriented Perl, with a simple extensible interface to write data adapters for other relational database schemas and flat file formats.