LinkinPath is a pathway mapping and analysis tool that enables users to explore and visualize the list of gene/protein sequences through various Flash-driven interactive web interfaces including KEGG pathway maps, functional composition maps (TreeMaps), molecular interaction/reaction networks and pathway-to-pathway networks. Users can submit single or multiple datasets of gene/protein sequences to LinkinPath to (i) determine the co-occurrence and co-absence of genes/proteins on animated KEGG pathway maps, (ii) compare functional compositions within and among the datasets using TreeMaps, (iii) analyze the statistically enriched pathways across the datasets, (iv) build the pathway-to-pathway networks for each dataset, (v) explore potential interaction/reaction paths between pathways, and (vi) identify common pathway-to-pathway networks across the datasets.