The identification of protein complexes is a fundamental challenge in interpreting protein-protein interaction data. Cross-species analysis allows coping with the high levels of noise that are typical to these data. The NetworkBLAST web-server provides a platform for identifying protein complexes in protein-protein interaction networks. It can analyze a single network or two networks from different species. In the latter case, NetworkBLAST outputs a set of putative complexes that are evolutionarily conserved across the two networks. AVAILABILITY: NetworkBLAST is available as web-server at: www.cs.tau.ac.il/~roded/networkblast.htm.