With the high speed development of the Internet,more and more users use web to obtain and issue medical information.Constructing a medical web application with the ASP.NET lists a series of complicated security problem to the structure designers and developers This paper discuss the security methods for the medical Web application designing, induding managing the user,testing and verifying the users, authorizing the users, encrypting private data,and filtering the input of the users. All methods are useful to plug up various security loopholes effectively and establish secure medical Web application.