Background: To assess the prevalence of allergic sensitization and to analyze patterns of sensitization to common inhalant and food allergens in a nationwide representative sample of children and adolescents in Germany. Methods: Data were collected from 2003 to 2006 within the KiGGS, the national Health Interview and Examination Survey covering a representative sample of 17,641 children and adolescents in Germany. Immunoglobulin E (IgE) antibodies to 20 specific allergens (11 inhalant and 9 food allergens) were quantitatively measured in a subsample of 12,988 KiGGS participants aged 3-17 years using the ImmunoCAP system. Serum concentrations ≥0.35 kU/l indicate sensitized participants. An exploratory factor analysis was performed in order to identify sensitization patterns. Results: Sensitization to at least 1 of the 20 tested allergens was detected in 40.2% [95% confidence interval (CI) 39.0-41.4] of the participants. The highest sensitization prevalences were found for pollen from Timothy grass (22.7%; 21.5-23.9) and rye (21.2%; 20.0-22.4). Sensitization was more prevalent in boys than in girls and prevalence increased generally with increasing age. We identified seven sensitization groups, namely (in descending order of magnitude) ‘Timothy grass/rye', ‘house-dust mites', ‘food/mugwort', ‘birch/apple', ‘animals', ‘cow's milk/egg white' and ‘moulds'. Conclusions: Allergic sensitization is common in German children and adolescents. The fact that sensitization potentially leads to clinically relevant allergic diseases stresses the public health relevance of this topic. Whether the grouping reflects the propensity for persons to be sensitized to multiple allergens within a group, or whether it is due to IgE cross-reactivity between different allergens of similar structure is still being discussed.