Systems-on-Programmable-Chip (SoPCs) include processors, memories and programmable logic that allow to catch multiple application requirements such as high performance, reconfigurability and low-costs. Due to these characteristics, they are also becoming very attractive for safety-critical applications. However, the issue of assessing the reliability they can provide and debugging the possible safety-related mechanisms they embed is still open. In this paper, we present a new fault-injection approach for evaluating the impact of transient faults in SoPCs. Fault-injection experiments are reported on a case study consisting of a web server implemented on a Xilinx Virtex-II FPGA embedding a PowerPC 405 and running the whole TCP/IP stack.