An important goal of systems biology is the identifica-tion and investigation of known and predicted protein-protein interactions to obtain more information about new cellular pathways and processes. Proteins inter-act via domains, thus it is important to know which domains a protein contains and which domains inter-act with each other. Here we present the Java TM pro-gram ProDGe (Protein Domain Gene), which visu-alizes existing and suggests novel domain-domain in-teractions and protein-protein interactions at the do-main level. The comprehensive dataset behind ProDGe consists of protein, domain and interaction information for both layers, collected and combined appropriately from UniProt, Pfam, DOMINE and IntAct. Based on known domain interactions, ProDGe suggests novel protein interactions and assigns them to four confi-dence classes, depending on the reliability of the un-derlying domain interaction. Furthermore, ProDGe is able to identify potential homologous interaction partners in other species, which is particularly help-ful when investigating poorly annotated species. We further evaluated and compared experimentally identi-fied protein interactions from IntAct with domain in-teractions from DOMINE for six species and noticed that 31.13% of all IntAct protein interactions in all six species can be mapped to the actual interacting domains. ProDGe and a comprehensive documenta-tion are freely available at http://www.cogsys.cs.uni-tuebingen.de/software/ProDGe.