The DNA sequence organization of a homogeneously staining region (HSR) in the germ line of Mus musculus was studied with DNA clones generated by microdissection and microcloning. Six HSR-derived microclones were selected and characterized by Southern blot hybridizations. Four represented single-copy mouse DNA sequences. They were amplified in the HSR as fragments co-migrating with the respective normal mouse sequence and as additional fragments of different mobilities. The copy number of co-migrating fragments was approximately 16 for each of the four sequences but the number of rearranged fragments varied. Two microclones contained DNA sequences not detectable in normal mouse genomes but present, and one of them amplified, in the HSR. The observations suggest that the HSR developed from a part of the mouse genome by alternating replication and rearrangement events, with a specific integration of putative foreign DNA sequences.