Genetic engineering has made the mouse an invaluable tool to address the function of individual genes in a targeted manner. Over the last decade it has become apparent that the genetic mouse strain background can significantly influence the phenotype of an engineered mouse. Therefore, it is essential to characterize the biology of the different wild-type background strains. In this study, we have compared mouse mammary gland involution in the 129S1 and C57BL/6 inbred strains and report significant differences at the molecular level with differential expression of Bcl2a1 (Bfl1), Trp53 (p53), Cebpb (C/EBP beta), and Cebpd (C/EBP delta). The C57BL/6 strain exhibits dynamic responses with induction of Trp53 and Cebpd and concomitant downregulation of Bcl2a1 during the first phase of involution. In contrast, expression of these genes does not change significantly in 129S1 mice. During the second phase, C57BL/6 glands contain more Cebpb than 129S1 glands. Nevertheless, involution proceeds morphologically with similar kinetics in both strains. The data demonstrate that the genetic response of mammary tissue varies significantly between 129S1 and C57BL/6. These results may provide a basis for the interpretation of strain-specific phenotypes in engineered mice and underline the importance of pure strains for large-scale expression studies with mutant mice.