A method and system for obfuscating computer code of a program to protect it from the adverse effects of malware is provided. The obfuscation system retrieves an executable form of the computer code. The obfuscation system then selects various obfuscation techniques to use in obfuscating the computer code. The obfuscation system applies the selected obfuscation techniques to the computer code. The obfuscation system then causes the obfuscated computer code to execute.