Gene Map Annotator and Pathway Profiler (GenMAPP) a free, open-source, stand-alone computer program is designed for organizing, analyzing, and sharing genome scale data in the context of biological pathways. GenMAPP database support multiple gene annotations and species as well as custom species database creation for a potentially unlimited number of species. Pathway resources are expanded by utilizing homology information to translate pathway content between species and extending existing pathways with data derived from conserved protein interactions and coexpression. A new mode of data visualization including time-course, single nucleotide polymorphism (SNP), and splicing, has been implemented with GenMAPP database to support analysis of complex data. GenMAPP also offers innovative ways to display and share data by incorporating HTML export of analyses for entire sets of pathways as organized web pages. In short, GenMAPP provides a means to rapidly interrogate complex experimental data for pathway-level changes in a diverse range of organisms.