Earlier epidemiologic studies within Germany found a higher frequency of allergic sensitization in West Germany. The reasons for that and the role of environmental factors in the process of allergic sensitization are not fully understood. This study aimed to determine the prevalence of positive skin-prick test results 5 years after unification and to investigate risk factors for allergic sensitization in preschool children. A total of 1235 children (5-6 years) from two West and five East German locations were skin-prick tested after the compulsory school entrance examination. Six common aero- (birch, grass, mugwort pollen, cat, HDM, alternaria) and two food allergens (egg, milk) were used and additional information was obtained by questionnaire. Of the tested children 23.3% exhibited at least one positive reaction. The prevalence of sensitization to the single allergens was as follows: grass (14.4%), birch (6.6%), mugwort pollen (4.5%), cat (8.5%), HDM (5.5%), alternaria (4.9%), egg (2.8%), and milk (3.9%). In the crude analysis significantly more children were sensitized in the East German city Magdeburg (40.2%) compared to the West German control region Borken (23.5%) (OR 2.20, CI 1.47-3.29). Dampness and visible molds were reported in 8.8% of all households, but significantly more often for East German apartments (10.3% versus West Germany 1.9%, OR 5.85, CI 2.55-16.53). Dampness and molds were associated with a higher frequency of sensitizations (40.6% versus 27.6% in unaffected homes). After controlling for sex, parental atopy, SES, family size, and smoking during pregnancy, this association remained statistically significant (OR 1.93, CI 1.19-3.12). With regard to single allergens, dampness and visible molds were significantly associated with sensitization to HDM (OR 3.37, CI 1.63-6.96), cat (OR 3.19, CI 1.11-5.74), and mugwort pollen (OR 2.86, CI 1.29-6.35). In addition, family size was inversely and linearly associated with the frequency of sensitization (OR for four, three, and two-person households: 1.10 (0.74-1.63), 1.57 (1.06-2.42), 2.70 (1.39-5.24), respectively, when compared to family size of five or more). Neither parental predisposition for atopic diseases nor parental education level influenced the prick test reactivity. We conclude that in addition to genetic predisposition, environmental factors like indoor climate and probably infectious stimuli (family size) play an important role in the process of allergic sensitization in children.