It is sometimes desirable to protect a design used in a PLD from being copied. If the design is stored in a different device from the PLD and read into the PLD through a bitstream, an unencrypted bitstream could be observed and copied as it is being loaded. According to the invention, a bitstream for configuring a PLD with an encrypted design includes unencrypted words for controlling loading of the configuration bitstream and encrypted words that actually specify the design.