BioNetBuilder is a Cytoscape plugIn that offers a user friendly interface to create biological networks integrated from several databases. Users can create networks for ~1000 different species, including most common model organisms and human. The interface offers different options to specify a set of initial genes/gene-products for which to find molecular interactions (including loading a simple text file, finding genes with specified Gene Ontology annotations, and finding genes whose common name match a given string). Depending on the user's computer capabilities, biological networks for whole organisms can also be created and displayed. Currently supported databases include: DIP, BIND, Prolinks, KEGG, HPRD, The BioGrid, and GO, among others. Users can set database parameters through the user interface to control which information from each database can be included in their networks (for example, interaction type, p-value, threshold, etc). BioNetBuilder also attaches to each gene cross reference IDs and URL links to public databases, including RefSeq, PIR, Prolinks, and The Yeast Resource Center.