Children suffering from atopic dermatitis frequently show allergen-specific sensitization. However, the corresponding IgE-recognition patterns have not yet been extensively characterized using multiallergen microarrays. To provide comprehensive, molecular IgE repertoires in paediatric patients with atopic dermatitis using microarray technology. Sera of 140 affected children were screened with a protein microarray containing a panel of 95 inhalant, food and staphylococcal antigen components. In addition, total serum IgE levels and further clinical parameters were recorded. At a mean total IgE level of 1528 kU/L, the number of sensitizations varied from 0 to 32 per patient, and regression analysis revealed a significant association between total IgE and the quantity of recognized antigens. A total of 78 single allergen and microbial components elicited at least one IgE response, while 11 plant and 13 non-plant molecules were recognized by more than 10% of patients. Specific IgE against Staphylococcus aureus could be detected in 14% of children. Sensitization rates against the studied allergen molecules differed significantly when stratified by age. Whereas reactivity against inhalant allergens and SEC was lowest in the youngest group (<24 months) reaching highest values in children ≥ 72 months, IgE responses against food allergen components peaked in younger age groups (0-48 months) and clearly declined in patients of higher age. The large amount of microarray data could be aggregated by centroid cluster analysis revealing valid allergen clusters possibly linked with higher disease severity as determined by multivariate analysis of covariance. Allergenic molecule microarray analysis can be regarded as a suitable research tool for large-scale IgE screening in infants and children with atopic dermatitis (AD). Still, further studies in well-defined populations are needed to exactly identify its tangible benefits in the diagnostic and therapeutic management of affected patients in daily clinical practice.