This paper describes an efficient methodology for testing dedicated clock lines in Field Programmable Gate Arrays (FPGAs). A H-tree based clocking architecture is proposed along with a test scheme. The H-tree architecture provides optimal clock skew characteristics. The H-tree architecture consumes at least 25% less of the routing resources when compared to conventional clock routing schemes. A testing scheme, which utilizes the partial reconfiguration capabilities of FPGAs through selective re-programming of the Complex Logic Blocks, to detect and locate faults in the clock lines is proposed