A method, in a server, implementing a moving target defense against cross-site scripting includes receiving a request for a web page, wherein the server has N versions of the web page each with a mutated version of JavaScript; selecting a web page of the N versions; and sending an indication of the mutated version of JavaScript associated with the web page in response to the request. Another method, in a client device, using a moving target defense against cross-site scripting includes requesting a web page; receiving an indication of a mutated version of JavaScript for the web page; and adjusting a JavaScript interpreter based on the mutated version of JavaScript for the web page.