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An autoindexing procedure is described that produces the indexing of diffraction data of aperiodic crystals. The procedure has been designed for indexing the data obtained with an area detector, but it can also be applied to data obtained with a single-point detector. The essential step in the indexing process is the ability to discriminate between reflections that fit to a reciprocal lattice, the satellite reflections and possible reflections that do not belong to this indexing. To achieve this goal, the refinement of the orientation matrix and the diffractometer parameters is made an intrinsic part of the process of indexing. The proposed autoindexing procedure has been implemented in a computer program called BAYINDEX. Successful application to data sets of three different one-dimensionally modulated structures, one two-dimensionally modulated structure and a periodic crystal is presented. Very good agreement between experimental and theoretical reflection positions is found. The indexing produced by BAYINDEX can serve as the basis for integration routines.