A novel core-based fingerprint indexing scheme for embedded systems is presented in this paper. Our approach is enabled by our new precise and fast core-detection algorithm with the direction map. It introduces the feature of CMP (core minutiae pair), which describes the coordinates of minutiae and the direction of ridges associated with the minutiae based on the uniquely defined core coordinates. Since each CMP is identical against the shift and rotation of the fingerprint image, the CMP comparison between a template and an input image can be performed without any alignment. The proposed indexing algorithm based on CMP is suitable for embedded systems because the tremendous speed up and the memory reduction are achieved. In fact, the experiments with the fingerprint database FVC2002 show that its speed for the identifications becomes about 40 times faster than conventional approaches, even though the database includes fingerprints with no core.