Domains are evolutionarily conserved sequence units and they are structural and functional building blocks of proteins. Interaction between two proteins typically involves binding between specific domains, and identifying interacting domain pairs is an important step towards thoroughly understanding protein function and evolution, constructing protein-protein interaction (PPI) networks, and analyzing pathway at the domain level. A number of interacting and/or functionally linked domain pairs have been identified and the information was organized and hosted in many domain-domain interactions (DDI) databases with the help of further mining experimental data and computational predictions from various input data. First, the 8 computational predicting methods used to acquire DDI data will be introduced. Then the introduction of DDI public databases, including 3DID, iPfam, InterDom, DIMA and DOMINE will be given. And finally, some examples are described about applications of DDI in computational predicting interacting protein pairs, assessment of the reliability for PPI, protein domain annotation, and in pathway study.