Sites for pairing and segregation of achiasmatic bivalents have been characterized in both male and female meiosis in Drosophila melanogaster. The major sex chromosome pairing site in male meiosis corresponds to the intergenic spacer repeats of the rDNA arrays, which are located in the heterochromatin of the X and Y. The sex chromosome pairing sites in females are also heterochromatic, but involve different repeated sequences. In males, weak pairing sites are widely distributed along euchromatin but not heterochromatin of chromosome 2, an autosome. One strong site for male meiotic pairing has been identified on chromosome 2; it overlaps with the his locus, which contains the repetitive structural genes for the histones. In females the sites for pairing of chromosome 4, another autosome, are restricted to the heterochromatin. Thus for both sex chromosomes and autosomes, sites for achiasmatic pairing are heterochromatic in females but euchromatic (except for the rDNA) in males. The possible roles of sequence repetition and of transcription in chromosome pairing are discussed.