This paper describes a novel method for online in-place detection and location of interconnects faults in SRAM-based FPGA systems. In safety critical systems like space probes, online checkers report misbehavior of sub-circuits within the system. When one such sub-circuit is reported to misbehave, the algorithm proposed in this paper performs run time reconfiguration (RTR) of LUTs in an attempt to detect and locate the interconnect faults, if any, within the faulty sub-circuit. Even in the subcircuit under test, at any given time, only a small section of the LUTs are used by the testing procedure. In this way the degradation of the application is kept at a minimum. The proposed algorithm is in-place, i.e. it does not alter the routing structure of the application. © 2003 IEEE.