In this paper, we overview general hardware architecture and a programming model of SRC-6E™ reconfigurable computers, and compare the performance of the SRC-6E machine vs. Intel . Pentium IV™. SRC-6E execution time measurements have been performed using three different approaches. In the first approach, the entire end-to-end execution time is taken into account. In the second approach, the configuration time of FPGAs have been omitted. In the third approach both configuration and data transfer overheads have been omitted. All measurements have been done for different numbers of data blocks. The results show that the SRC-6E can outperform a general-purpose microprocessor for computationally intensive algorithms by a factor of over 1500. However, overhead due to configuration and data transfer must be properly dealt with by the application or the system?s run-time environment to achieve the full throughput potential. Some techniques are suggested to minimize the influence of the configuration time and maximize the overall end-to-end system performance.