Mechanistic and regulatory aspects of meiotic chromosome pairing and segregation have received increasing attention in recent years. This review is concerned with the role of chromosomal sites and chromosome organization in pairing and sperm development in Drosophila. Two major topics are reviewed. The first concerns the distribution and identification of meiotic pairing sites in male Drosophila. Cytogenetic data show that pairing sites are distributed widely in the euchromatin of autosomes but are absent from centromeric heterochromatin. The reverse distribution holds for the X, where the major pairing site is located in the central region of the centric heterochromatin, co-mapping with the rDNA locus. Recent transgenic studies have demonstrated that this pairing site consists mainly of a 240-bp repeated sequence in the intergenic spacers of the rDNA repeats. These spacer repeats contain RNA polymerase I promoters, which must be functional for the repeats to have pairing activity, suggesting a mechanistic connection between pairing and transcription. The general idea that pairing sites coincide with transcribed sequences is discussed. The second major topic involves the effects of sex chromosome rearrangements on spermiogenesis. A variety of rearrangements involving the sex chromosomes, including heterochromatic deletions and translocations with autosomes, have been shown to lead either to meiotic drive or to sterility. Recent evidence strongly implicates the X chromosome pairing site in the etiology of these effects. These findings are discussed in terms of a novel model that interprets the spermiogenic disruptions associated with sex chromosome rearrangements as resulting from disabling of spermatids due to triggering of a checkpoint concerned with monitoring chromosome alignment at meiotic metaphase.