Background: There is a high prevalence of allergies in Germany, with approximately 20% of the population having at least one allergy and only about 10% of these being treated adequately. We conducted a cross-sectional study in a rural area of Bavaria (Southern Germany) to evaluate the prevalence of allergies and their treatment, because research regarding this topic is currently limited. Methods: Data were collected in 10 offices of non-dermatological doctors using a self-filled questionnaire to ask participants about allergies and treatment. Results: A total of 641 questionnaires were appropriate for analysis. The prevalence of allergies in the Bavarian countryside was higher than that reported for Germany (37.3% vs. 20.0%). Furthermore, almost a third (30.4%) of allergies were not treated at all. The most frequently consulted therapist was found to be a general practitioner. Conclusions: Based on the study results, there is a need for prevention programs and establishment of treatments for certain allergies to minimize long-term health effects. Moreover, more studies are needed to analyze the prevalence of allergies in farmers who had a higher prevalence of allergies compared to previously reported prevalence in literature reviews. Trial registrations: The study was approved by the ethical review committee of the Technical University Munich (EC number 548/16S).