Systems and methods for repairing cross-linked biometric records receive a set of biometric records. Each biometric record contains at least one biometric sample in a non-textual modality. One or more of the biometric records in the set of biometric records is potentially a cross-linked biometric record having at least two biometric samples that are associated with different individuals. Crosslink resolution is performed on the set of biometric records by searching for a match between a biometric sample in a given non-textual modality of a given biometric record with each biometric sample of the same given non-textual modality in each of the other biometric records in the set of biometric records. During the crosslink resolution, biometric sample may be removed from one biometric record and merged with another biometric record.