Surface-spread, silver-stained primary spermatocytes from individuals of the Sitka deer mouse (Peromyscus sitkensis) were analyzed by electron microscopy. Pairing of the X and Y chromosomes is initiated at early pachynema and is complete by mid pachynema. The pattern of sex chromosome pairing is unique in that it is initiated at an interstitial position, with subsequent synapsis proceeding in a unidirectional fashion towards the telomeres of the homologous segments. One-third the length of the X and two-thirds the length of the Y are involved in the synaptonemal complex of the sex bivalent. Various morphological complexities develop in the heteropycnotic (unpaired) segments as pachynema progresses, but desynapsis is not initiated until diplonema. Analysis of C-banded diakinetic nuclei indicated that sex chromosome pairing involves the heterochromatic short arm of the X and the long arm of the heterochromatic Y. An interstitial chiasma between the X and Y was observed in the majority of the diakinetic nuclei. The observation of a substantial pairing region and chiasma formation between the sex chromosomes of these deer mice is interpreted as indicating homology between the short arm of the X and the long arm of the Y.