The C578L/6 (B6) is one of the oldest inbred mouse strains. It has been widely used as control strain in metabolism research for many decades. Preliminary data from our lab indicated that C57BL/6JRj mice are not responding to diet induced obesity. Therefore, the aim of this study was to compare the two different B6 substrains, C57BL/6NTac and C57BL/6JRj, in regard to their response to diet induced obesity (DIO) and to investigate genetic differences which may explain such phenotypic differences. Sixteen male mice of C57BL/6NTac and C57BL/6JRj were fed a high fat diet (HFD) or standard chow diet (SD) for 10 weeks. Phenotypic characterization included measurements of bodyweight, physical activity, food intake and relative epigonadal fat mass. Genetic differences between both substrains were analyzed using a panel of 1449 single nucleotide polymorphism (SNP) markers. Our study revealed that C57BL/6JRj mice are protected against 010 independently from food intake and physical activity. Genetic SNP analysis among C57BL/6 mice identified genetic differences in at least 11 SNPs. Our data strongly support the importance of attention on the genetic background in obesity research. (C) 2011 Elsevier Inc. All rights reserved.