The yeast Saccharomyces cerevisiae has a single tandem array of 100 ribosomal RNA (rRNA) genes. We have cloned and characterized a junction between the centromere-distal end of this array and the adjacent single-copy chromosomal sequences. We have shown that the junction occurs within the nontranscribed region of the repeat. By mapping the junction, we have found that the 35S rRNA precursor is transcribed toward the centromere while the 5S rRNA is transcribed away from the centromere. We have also shown that different yeast strains can have different single-copy sequence at the junction.