The effects of the nonpseudoautosomal region of the Y chromosome (YNPAR) on hippocampal morphology have been investigated in the inbred mouse strains NZB/B1NJ and CBA/H, using comparisons between the two parentals and their respective congenics N.H-YNPAR and H.N-YNPAR. Results obtained depend upon the hippocampal variable measured. YNPAR had no effect on the sizes of the stratum oriens, hilus, or mossy fiber terminal fields (both suprapyramidal and intra- and infrapyramidal). However, in interaction with the strain background, it affected the strata lacunosum-moleculare, radiatum, and pyramidale. Possible relationships among gene(s), mossy fiber terminal fields, and intermale aggression are discussed.