A significant quantitative trait locus (QTL) for murine litter size, Lsq1, was previously identified on chromosome 7 in the female backcross progeny of ♀(♀C57BL/6J × ♂RR/Sgn) × ♂RR/Sgn (BRR mice). In the present study, QTL mapping analysis was performed for the same trait in the female backcross progeny of ♀(♀RR/Sgn × ♂C57BL/6J) × ♂RR/Sgn (RBR mice), and Lsq1 was identified again. As litter size is significantly larger in BRR mice than that in RBR mice, the potential effect of grandparental cross direction was indicated. QTL mapping analysis of combined data from BRR and RBR mice showed that Lsq1 was split into two loci: Lsq1-1 and Lsq1-2. The RR/Sgn strain-derived allele was associated with reduced litter size at both loci. Lsq1-1 and Lsq1-2 exhibited significant effects on the number of stillbirths in RBR mice but not in BRR mice, and the RR/Sgn strain-derived allele was associated with increased stillbirths at both loci. Therefore, the effects of Lsq1-1 and Lsq1-2 suggest that the number of stillbirths depends on the grandparental cross direction and that the smaller litter size in RBR mice is a consequence of increased stillbirths. Lsq1-1 and Lsq1-2 are suggested to be novel QTL associated with murine litter size.