Analysis of a radiation-induced minichromosome using classical cytogenetic techniques and fluorescence in situ hybridization (FISH) has shown this element to be composed primarily, if not entirely, of repeat sequence DNAs that are common to the ends of all chromosomes in the mouse genome. This novel chromosome has been used to examine further the role of centromeric and telomeric DNA sequences in the initiation of homologous chromosome pairing and synapsis in female germ cells. In pachytene oocytes of a fetus carrying two copies of the minichromosome, it was found that these elements were collocalized, but had not undergone synapsis, in half of the cells analysed. The minichromosomes formed a synaptonemal complex in approximately 14% of oocytes. Overall, therefore, the minichromosomes showed a surprising ability to achieve the first phase of homologous chromosome pairing, i.e. collocalization, despite their dearth of chromosome-specific DNA sequences. It is suggested that this collocalization largely results from the tendency of mouse chromosome ends to form centromeric and telomeric clusters at zygotene. The observations here provide support for the proposition that clustering of chromosome ends in early meiosis fosters pairing interactions and synapsis.