The first follow-up of the German Health Interview and Examination Survey for Children and Adolescents (KiGGS Wave 1) was conducted from 2009 to 2012 as a combined cross-sectional and longitudinal study and provides, among other things, data on allergic diseases. Data collection was carried out by telephone interviews. In total, 6,093 girls and 6,275 boys were included, among them 4,455 newly recruited 0- to 6-year-olds (response 38.8%) and 7,913 KiGGS follow-up participants aged 7-17 years (response 72.9%). Based on parent reports, 15.6% (95% confidence interval 14.7-16.5) of children and adolescents aged 0-17 years were currently affected by at least one atopic disease. The 12-month prevalence rates of hay fever, atopic dermatitis, and asthma were 9.1% (8.4-9.8), 6.0% (5.4-6.6), and 4.1% (3.6-4.6), respectively. In all, 2.2% (1.9-2.6) of the children and adolescents were currently suffering from contact dermatitis. Compared with the baseline KiGGS survey from 2003 to 2006, a higher percentage of participants reported the occurrence of asthma within the past 12 months in the recent KiGGS Wave 1 (4.1 vs. 3.2%; p = 0.0034). The total increase is mainly due to higher prevalence rates among 0- to 6-year-olds, especially in girls. Higher 12-month prevalence rates can be also observed for hay fever among 0- to 6-year-olds, especially in girls, although the total increase is not statistically significant (9.1 vs. 8.3%; p = 0.08). There was a declining trend for atopic dermatitis: 6.8% (2003-2006) vs. 5.4% (2009-2012); p = 0.0015.