It is sometimes desirable to encrypt a design for loading into a PLD so that an attacker may not learn and copy the design as it is being copied into the PLD. According to the invention, a method for generating a bitstream for storing an encrypted design begins by generating an unencrypted bitstream including bits representing the design and bits that control loading of the design. The bits representing the design are encrypted and are combined with the bits that control loading, which are not encrypted.