Both light and electron microscopy were used to study the pairing behavior of the sex chromosomes of the harvest mouse, Micromys minutus, in surface-spread pachytene spermatocytes. The XY pairing pattern is very exceptional in that the site of synaptic initiation is located interstitially in the short arms of the X and the Y, next to their centromeric regions. From this tiny euchromatic site, synapsis proceeds unidirectionally along the homologous heterochromatic short arms of the X and the Y toward the ends of the chromosomes. After pairing of the short arm is concluded, synapsis begins between the nonhomologous long arms of the X and the Y in the immediate vicinity of the centromeres and progresses unidirectionally toward the end of the long arm of the Y. A synaptic complex develops between the constitutive heterochromatin of the long arm of the Y and the euchromatin of the long arm of the X. Analysis of C-banded and distamycin A/DAPI-stained diakineses revealed a trefoil-like XY bivalent, which was interpreted to be the result of an interstitial chiasma occurring in the paired short arms of the X and the Y. A conspicuous, electron-dense body, about 1 micron in diameter, was found closely associated with the centromeres of the X and the Y in numerous pachytene spermatocytes. A review of the literature showed that comparable XY-associated bodies have been found in only eight other mammals to date.