Previously, we reported a recombination-prone human alphoid-like repetitive DNA (Sau3A family) which is characterized by abundance in the extrachromosomal fraction and restriction fragment length polymorphism. We suggested a specific homologous recombination to be responsible for the DNA excision from the chromosomes and also the sequence rearrangement in the chromosomes. In order to investigate the nature of the recombination further, 8 different clones were obtained which hybridized with Sau3A probe among over 1,500 extrachromosomal DNA clones. Restriction mapping and nucleotide sequence analyses showed two to be Sau3A monomers and dimers, four Sau3A recombinants, as observed previously, one a recombinant of the Sau3A-related sequence on chromosome 17, and one a new Sau3A-related sequence. Sequence analyses of the recombination junctions in the recombinant clones indicated a specific homologous recombination also to be responsible for all but one clone. The molecular mechanism and biological significance associated with the recombination are discussed.