The 3D-interologs database records the evolution of protein-protein interactions database across multiple species. Based on "3D-domain interologs" and a new scoring function, we infer 173,294 protein-protein interactions by using 1,895 three-dimensional (3D) structure heterodimers to search the UniProt database (4,826,134 protein sequences). For a protein-protein interaction, the 3D-interologs database shows functional annotations (e.g. Gene Ontology annotations), interacting domains and binding models (e.g. hydrogen-bond interactions and conserved residues). Additionally, this database provides couple-conserved residues and the interacting evolution by exploring the interologs across multiple species. Experimental results reveal that the proposed scoring function obtains good agreement for the binding affinity of 275 mutated residues from the ASEdb. The precision and recall of our method are 0.52 and 0.34, respectively, by using 563 non-redundant heterodimers to search on the Integr8 database (549 completely deciphered genomes). The proposed method can infer many of the interactions that would not have been identified from sequence similarity alone. The 3D-interologs database comprises 15,024 species and 283,980 protein-protein interactions, including 173,294 interactions (61%) discovered from 3D-domain interologs and 110,686 interactions (39%) summarized from the IntAct database. The 3D-interologs database is available at http://3D-interologs.life.nctu.edu.tw.