The mechanisms determining which parental haplotype is selected in (CBA X B10) (k X b)F1 female mice for major histocompatibility complex (H-2) restricted, male-specific (H-Y), immune, cytotoxic T-cell (Tc-cell) responses, was investigated. The data show that haplotype preference is variable, and may be directed towards one, both, or neither of the parental haplotypes. This preference is reflected in the precursor or frequency of memory Tc cells as measured by limiting dilution assays. It was further shown that maternal influence, antigen dose, route of immunization, and a feedback mechanism on the stimulator cells in vivo could not influence haplotype preference or its observed variability. Evidence for cross-reactive killing by H-2k and H-2b H-Y immune Tc cells on H-2b and H-2k allogeneic targets, respectively,, (i.e., the independent haplotype of the other parent of the F1 mice), provide evidence for natural tolerance as a possible mechanism to explain haplotype preference.