A new binary joint transform correlator algorithm is presented which uses the discrete cosine transform technique to process the joint transform power spectrum. This binary joint transform correlator can compare a target fingerprint with four reference fingerprints. Compared with other joint power spectrum processing method such as slide-window local median threshold method, the correlator using this technique has better performance in terms of output peak-to-noise ratio, peak intensity and discriminate rate. The result of optical-electrical hybrid experiment has shown that this technique can greatly improve the discrimination ability of multiple fingerprint identification system.