BackgroundFilaggrin is a structural protein that has attracted increasing interest over the past decade for its role in the pathogenesis of human atopic dermatitis (AD). Null mutations in its sequence are considered risk factors in the development of AD.Hypothesis/ObjectivesTo investigate canine filaggrin mRNA and protein expression in the skin of atopic beagles with experimentally induced AD compared with breed‐matched healthy control dogs.MethodsAll dogs were environmentally challenged for 3 days consecutively with allergens to which the atopic dogs had been sensitized. Skin biopsy specimens were taken from six healthy and seven atopic beagles before and after allergen challenge. Canine filaggrin mRNA was measured using quantitative real‐time PCR. Indirect immunofluorescence was used to localize the filaggrin protein in canine skin. Analysis of variance with Tukey's multiple comparison test (over‐time effect) and unpaired Student's t‐test (treatment effect) were used. Values of P ≤ 0.05 were considered significant.ResultsAnalysis of variance showed a significantly higher expression of filaggrin mRNA in atopic dogs compared with healthy control dogs (P = 0.004 on day 3 and P = 0.01 on day 10) and a decreased mRNA expression on day 3 in healthy control dogs (effect of time, P = 0.006). On blinded evaluation, filaggrin immunofluorescence was distributed homogeneously in the stratum granulosum and the stratum corneum in healthy dogs. Atopic dogs showed a patchy immunofluorescence pattern, which was exacerbated after environmental challenge.Conclusions and clinical importanceAltered epidermal filaggrin mRNA expression and protein distribution was detected in this experimental model.