This paper describes the formal verification of the Merchant Registration phase of the Secure Electronic Transactions (SET) protocol, a realistic electronic transaction security protocol which is used to protect the secrecy of online purchases. A number of concepts, notations, functions, predicates, assumptions and rules are introduced. We describe the knowledge of all legal participants, and a malicious spy, to assess the security of the sub-protocol. Avoiding search in a large state space, the method converges very quickly. We implemented our method in the Isabelle/Isar automated reasoning environment, therefore the whole verification process can be executed mechanically and efficiently. Keywords Formal verification - electronic transaction protocol - knowledge-based system This work was supported by EC, EPSRC, the National Natural Science Foundation of China (No.60496320, 60496321), and Hong Kong K C Wang Education Foundation.Xiao-Qi Ma graduated from Nanjing University of Science and Technology, China, in 1997. He received his Master’s degree from the Institute of Software, Chinese Academy of Sciences in 2003. He is currently a PhD student at the University of Reading. His research interests include computer network security, knowledge-based systems, and operating systems.Xiao-Chun Cheng obtained his PhD in 1996. He has worked as a lecturer at the University of Reading since 2000. He is a guest professor at North East Normal University and Beijing Normal University. His research interests include theoretical and applied aspects in decision support systems, knowledge-based systems and intelligent systems.