PURPOSE: The Society of Thoracic Surgeons Congenital Heart Surgery Database (STS-CHSD) is the largest Registry in the world of patients who have undergone congenital and pediatric cardiac surgical operations. The Congenital Heart Surgeons' Society Database (CHSS-D) is an Academic Database designed for specialized detailed analyses of specific congenital cardiac malformations and related treatment strategies. The goal of this project was to create a link between the STS-CHSD and the CHSS-D in order to facilitate studies not possible using either individual database alone and to help identify patients who are potentially eligible for enrollment in CHSS studies. METHODS: Centers were classified on the basis of participation in the STS-CHSD, the CHSS-D, or both. Five matrices, based on CHSS inclusionary criteria and STS-CHSD codes, were created to facilitate the automated identification of patients in the STS-CHSD who meet eligibility criteria for the five active CHSS studies. The matrices were evaluated with a manual adjudication process and were iteratively refined. The sensitivity and specificity of the original matrices and the refined matrices were assessed. RESULTS: In January 2012, a total of 100 centers participated in the STS-CHSD and 74 centers participated in the CHSS. A total of 70 centers participate in both and 40 of these 70 agreed to participate in this linkage project. The manual adjudication process and the refinement of the matrices resulted in an increase in the sensitivity of the matrices from 93% to 100% and an increase in the specificity of the matrices from 94% to 98%. CONCLUSION: Matrices were created to facilitate the automated identification of patients potentially eligible for the five active CHSS studies using the STS-CHSD. These matrices have a sensitivity of 100% and a specificity of 98%. In addition to facilitating identification of patients potentially eligible for enrollment in CHSS studies, these matrices will allow (1) estimation of the denominator of patients potentially eligible for CHSS studies and (2) comparison of eligible and enrolled patients to potentially eligible and not enrolled patients to assess the generalizability of CHSS studies.