Background: The NC/Nga mouse spontaneously develops eczematous atopic dermatitis (AD)-like skin lesions when maintained under conventional conditions, but not when kept under specific pathogen-free (SPF) conditions. Hence, there is a need for an AD model in mice housed under SPF conditions, as this is mandatory for research animals in many countries. Methods: We evaluated the use of the hapten FITC as an inducer of AD-like disease in NC/Nga and BALB/c mice maintained under SPF conditions. Mice were either untreated or treated with tacrolimus or betamethasone. Using the software Computer Assisted Stereological Toolbox as a stereological method, the mice were sensitized to FITC and the histological efficiency of disease induction with regard to inflammation and CD4+ and CD8+ lymphocytes, in addition to mast cells, was evaluated. The method was validated by comparison to a conventional semiquantitative observer-dependent method. Results: Our findings prove that FITC does indeed induce AD-like lesions in NC/Nga mice with regard to the histological appearance of the mice. However, when evaluating the immunological response in the affected areas of the mice with regard to the CD4/CD8 ratio and the effect of treatment, we found that the immune response in the NC/Nga mice differed from AD skin lesions in humans in certain aspects. Conclusions: These results emphasize the importance of an assessment of not only the histological but also the immunological appearance of the skin when evaluating AD-like disease in mice as a model for AD in humans.