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Summary: Regulatory T (Treg) cell‐specific deletion of a gene of interest is a procedure widely used to study mechanisms controlling Treg development, homeostasis and function. Accordingly, several transgenic mouse lines have been generated that bear the Cre recombinase under control of the Foxp3 promoter either as a random transgene insertion or knocked into the endogenous Foxp3 locus, with the Foxp3YFP‐Cre strain of mice being one of the most widely used. In an attempt to generate Treg cells that lacked expression of the insulin receptor (Insr), we crossed Foxp3YFP‐Cre mice with Insrfl/fl mice. Using a conventional two‐band PCR genotyping method we found that offspring genotypes did not correspond to the expected Mendelian ratios. We therefore developed a quantitative PCR‐based genotyping method to investigate possible ectopic recombination outside the Treg lineage. With this method we found that ~50% of the F1‐generation mice showed evidence of ectopic recombination and that ~10% of the F2‐generation mice had germline Cre recombination activity leading to a high frequency of offspring with global Insr deletion. Use of the quantitative PCR genotyping method enabled accurate selection of mice without ectopic recombination and only the desired Treg cell‐specific Insr deletion. Our data highlight the need to use genotyping methods that allow for assessment of possible ectopic recombination driven by the Foxp3YFP‐Cre allele, particularly when studying genes that are systemically expressed. [ABSTRACT FROM AUTHOR]