Background and aim The Berlin Fat Mouse Inbred line (BFMI) is a model for obesity and related pathologies such as insulin resistance and fatty liver. The aim of this study was to identify genetic variants associated with plasma and pancreatic insulin content in two sub-strains of the BFMI (BFMI861-S1 and BFMI861-S2). These lines are genetically close related but differ in several metabolic phenotypes (e.g. blood glucose concentration, plasma insulin, and body weight).