With the completion of the Genome Sequencing Project, it is now possible to rapidly and accurately determine the frequency and position of a particular repeat sequence in the Caenorhabditis elegans genome. Several repeat sequences with a variety of characteristics have been examined and with few exceptions they show a near-random distribution throughout the genome. We characterized several genes near the left end of Chromosome III in the C. elegans genome, and found a 24-bp minisatellite repeat sequence present in the introns of two unrelated genes. This prompted a search of the databank for other occurrences of this sequence. Multiple copy arrays of this repeat are all located on the same autosome and fall in two clusters: one near the left end, and one in the central region separated by ∼10 Mb. There are >200 copies of this repeat on the chromosome. This euchromatic repeat sequence seems unrelated to gene expression, is absent from homologous sites in a related species, is unstable in Escherichia coli, and is polymorphic between different wild isolates of C. elegans. Most CeRep25B units in the array match the consensus sequence very well, suggesting that either this repeat originated quite recently or its sequence is functionally constrained. Although chromosome-specific repeat sequences have been reported previously in many organisms, such sequences are usually structural and heterochromatic (e.g., centromeric α-satellite) or on the mammalian sex chromosomes. This report describes the first confirmed instance from a whole genome sequencing project of an autosomal euchromatic chromosome-specific minisatellite repeat.