MOTIVATION: Exploration and analysis of interactome networks at systems level requires unification of the biomolecular elements and annotations that come from many different high-throughput or small-scale proteomic experiments. Only such integration can provide a non-redundant and consistent identification of proteins and interactions. APID2NET is a new tool that works with Cytoscape to allow surfing unified interactome data by querying APID server (http://bioinfow.dep.usal.es/apid/) to provide interactive analysis of protein-protein interaction (PPI) networks. The program is designed to visualize, explore and analyze the proteins and interactions retrieved, including the annotations and attributes associated to them, such as: GO terms, InterPro domains, experimental methods that validate each interaction, PubMed IDs, UniProt IDs, etc. The tool provides interactive graphical representation of the networks with all Cytoscape capabilities, plus new automatic tools to find concurrent functional and structural attributes along all protein pairs in a network. AVAILABILITY: http://bioinfow.dep.usal.es/apid/apid2net.html. SUPPLEMENTARY INFORMATION: Installation Guide and User's Guide are supplied at the Web site indicated above.