Reverse transcriptase qPCR is the most common method to determine and compare mRNA expression levels and relies on normalization using reference genes. The expression levels of the latter, however, are themselves often variable between experimental conditions, thus compromising the results. Using the geNorm algorithm, we have examined seven genes with respect to their suitability as reference genes for gene analysis in mouse models of skin inflammation, using the antibody transfer model of epidermolysis bullosa acquisita and in the Aldara™ -induced psoriasiform dermatitis. Our results indicate that the combination of at least 2-3 reference genes is required for stable normalization. Notably, the expression of reference genes changed when comparing lesional skin of both models or when comparing lesional to non-lesional skin within one model. This highlights the need for precise selection of reference genes dependent on the specific experimental setup.