An apparatus for and method of programming a programmable logic device, the programmable logic device comprising a plurality of serially connected programmable logic regions. The method comprises the steps of receiving initial programming data for programming the plurality of serially connected programmable logic regions and receiving transformation data related to the presence and location of at least one faulty serially connected programmable logic region. The method also comprises the steps of generating bypass programming data which, in use, renders a serially connected programmable logic region logically invisible and generating effective programming data by incorporating, using information found in the transformation data, the bypass programming data into the initial programming data. Finally, the method comprises the step of programming the programmable logic device using the effective programming data such that the at least one faulty serially connected programmable logic region is programmed with the bypass programming data.