Recently one of my collegues was trying to create a Web Setup project for an application in VS2005 and he commented "I can't add the Primary Output of the application to the setup, just the content." This is where VS2005 (or actually ASP.NET 2.0) differs from VS2003, so I explained that this was normal behavior and that his application didn't need to have an application assembly because ASP.NET 2.0 compiles everything on the fly. His reply was that you wouldn't want to have your source code sitting in the production enviroment, and he is absolutely right. The solution to this is precompiling your applications with aspnet_compiler.exe. This packages all your files, inlcuding the contents of your .aspx files in an assembly which is used to run the site. The .aspx files are still there, but these are just placeholder files with no contents. By default the .aspx files can't be edited (well, you can but that doesn't change what is sent to the browser), but this can be controlled. Checkout the MSDN article How to: Precompile ASP.NET Web Sites for Deployment on how to use aspnet_compiler.exe. For a complete rundown of precompilation see ASP.NET Web Site Precompilation.