The probability of faults, and especially transient faults, occurring in the field is increasing with the evolutions of the CMOS technologies. It becomes therefore crucial to predict the potential consequences of such faults on the applications. Fault injection techniques based on the high level descriptions of the circuits have been proposed for an early dependability analysis. In this paper, a new approach is proposed, based on emulation and run-time reconfiguration. Performance evaluations and practical experiments on a Virtex development board are reported.