Background: Allergies and asthma exhibit a growing health problem in the world. Sparse data are available about the prevalence of allergic sensitization in Estonia and Eastern Europe as well. We studied the prevalence of allergic sensitization, the associations between respiratory symptoms and allergic sensitization, and the influence of age, gender, area of residence, number of siblings and other demographic attributes on allergic sensitization in the population aged 17–69 years. Methods: We conducted a cross-sectional study with 1,346 randomly selected participants distributed in 3 geographically and culturally distinct areas of Estonia. Sensitization to 15 aeroallergens was assessed by skin prick tests. The study also included a structured interview. Results: The total prevalence of allergic sensitization was 33.0%. When estimated in patients aged 20–44 years, the prevalence was 38.5%. The most common sensitizer was cockroach followed by storage mites, while sensitization to cat, dog or pollen (common sensitizers in Scandinavian countries) was low. Allergic sensitization was significantly more common in urban and suburban compared with rural areas. Storage mites were the most common sensitizers in rural areas. Living in urban or suburban areas before the age of 5 significantly increased the risk for positive skin prick tests to several allergens. Conclusions: A higher prevalence of allergic sensitization than previously believed was found. Cockroach and storage mite allergens are suggested to be included in the routine investigation panel in Estonia.