Clinical decision support (CDS) for atrial fibrillation is expected to ease the implementation of often-complex guidelines for atrial fibrillation and anticoagulation. Most clinical decision support systems (CDSS) for anticoagulation are stand-alone systems that do not integrate with electronic medical records (EMR). We have developed an architecture that consists of a computerized CDS that can integrate with multiple EMRs and multiple patient health records (PHRs). The design process revealed some significant issues that were resolved through systematic business/clinical analysis and creative clinical design in the diagnostic and treatment domains. Key issues identified and resolved include: 1) how to correctly allocate existing patients into various CDSS states (e.g., MAINTENANCE, HOLD, DISCONTINUE, etc), 2) identify when a patient becomes eligible for CDSS guidance over time, 3) how the CDSS maintains information about the patient's anticoagulation state and 4) how to transform vague human-readable concepts to explicit computable concepts. The management of anticoagulation for atrial fibrillation is no easy task and we believe our architecture will improve patient care at all levels and ultimately better balance the reduction of stroke risk while minimizing harms from major bleeding. In addition, the architecture presented is scalable to other treatment guidelines and is scalable to multiple EMRs and PHRs, making it suitable for use in a platform approach.