A fingerprint authentication system, comprising: a fingerprint data acquisition device which acquires fingerprint data; an index determination device comprising a plurality of stages of index determination units which determine index data being a set of indexes comprising one class and conditions; and a registration part in which the fingerprint data (FD, TFD) is registered according to the index data, wherein each index determination unit determines an index of the index data corresponding to which class the fingerprint data is to be classified, or to which condition the fingerprint data satisfies, and the index determination device provides the index data associated with the fingerprint data to the registration part, and the registration part registers the fingerprint data in a group of a plurality of groups corresponding to the index data, wherein, in case the difference between the numbers of pieces of fingerprint data registered in adjacent groups of a same stage is equal to or greater than 50% of the number of pieces of fingerprint data registered in one group of the plurality of groups of the same stage, the order of the set of indexes is reconfigured by interchanging an index of the same stage and an index in a lower stage and this process of changing indexes is repeated until the pieces of fingerprint data are registered into groups of approximately equal number of pieces of data, and wherein the class includes LOOP, when the fingerprint has a pattern of loops, WHORL, when the fingerprint has a pattern of circles, or ARCH, when the fingerprint has a pattern of arches, and the conditions include number of lines, interval between lines or angle of a line concerning a short line, a bar line, a hair line or an island line of the fingerprint. a fingerprint data acquisition device which acquires fingerprint data; an index determination device comprising a plurality of stages of index determination units which determine index data being a set of indexes comprising one class and conditions; and a registration part in which the fingerprint data (FD, TFD) is registered according to the index data, wherein each index determination unit determines an index of the index data corresponding to which class the fingerprint data is to be classified, or to which condition the fingerprint data satisfies, and the index determination device provides the index data associated with the fingerprint data to the registration part, and the registration part registers the fingerprint data in a group of a plurality of groups corresponding to the index data, wherein, in case the difference between the numbers of pieces of fingerprint data registered in adjacent groups of a same stage is equal to or greater than 50% of the number of pieces of fingerprint data registered in one group of the plurality of groups of the same stage, the order of the set of indexes is reconfigured by interchanging an index of the same stage and an index in a lower stage and this process of changing indexes is repeated until the pieces of fingerprint data are registered into groups of approximately equal number of pieces of data, and wherein the class includes LOOP, when the fingerprint has a pattern of loops, WHORL, when the fingerprint has a pattern of circles, or ARCH, when the fingerprint has a pattern of arches, and the conditions include number of lines, interval between lines or angle of a line concerning a short line, a bar line, a hair line or an island line of the fingerprint.