A method and system for centralized automated reconciliation of investment manager and related custody accounts makes use of computer hardware and software in a service bureau environment to receive information and records electronically from fund managers and custodian banks in different formats, to reformat the files for inputting to the system, and to perform the reconciliation process in a uniform manner. The system also allows one or both of fund managers and custodians to establish matching rules, to view the results of the matching process, to track the investigation process for unmatched records, and to manually match unmatched records.