Abstract: Method and apparatus for tolerating defects in a programmable logic device (PLD). A PLD includes a plurality of configurable logic elements and interconnect resources, wherein one or more of the configurable logic elements and interconnect resources have circuit defects. A design program is executed that is suitable for run-time reconfiguration of the PLD. The design program includes executable code that specifies a circuit design and generates a configuration bitstream that implements the circuit design on the programmable logic device. The design program also includes code that selectively skips the configurable logic elements and interconnect resources that contain the defects. In various embodiments, an individual configurable logic element, an entire row, or an entire column of elements can be skipped responsive to an input parameter.