Minisatellites provide very informative systems for analyzing processes of tandem repeat DNA turnover in humans. The mouse genome also contains authentic minisatellites, but none has yet been found to show high levels of instability. Indirect evidence using minisatellite variant repeat mapping by PCR in Mus musculus subspecies suggested that mouse minisatellites mutate at a rate below 10(-3) per gamete and mainly by intra-allelic events. This is in sharp contrast to the complex interallelic mutations observed at high frequency at some human loci. To define more directly the turnover mechanisms and rates of instability at one of the most variable mouse minisatellites (MMS80), we used size-enrichment small-pool PCR (SESP-PCR) to recover de novo mutant alleles from sperm DNA from homozygous BALB/cJ mice and from strain DHA heterozygotes. The sperm mutation rate at MMS80 was extremely low, at or below 5 x 10(-6) per sperm. Comparison of progenitor and mutant allele structures showed that these rare mutants had arisen by simple and primarily, if not exclusively, intra-allelic mutation events. These results suggest a fundamental difference in turnover mechanisms at minisatellites between mice and human.