We have determined the complete nucleotide sequence of a 3564 bp EcoRI fragment which represents a major component of the human Y-chromosome specific repeated DNA family (DYZ1). Sequencing result showed a tandem array of pentanucleotides after five nucleotides were inserted or deleted at four positions. 229 out of the 713 pentanucleotides were TTCCA, and 297 were its single-base substituents. Southern hybridization analyses of male genomic DNAs showed that several endonuclease cleavage sites were located at intervals of 3.56kb in the DYZ1 locus. This indicates that the DYZ1 repeated DNA family evolved and expanded by unequal crossovers which occurred at distances of 3.56kb. As there is a uniformly distributed array of pentanucleotides on this locus, it is not a sequence homology that determines the distance of unequal crossovers. A higher order of chromatin structure may be involved in the determination of distance in unequal crossovers.