Background: Atopic patients are exceptionally sensitive to airborne allergens. Sensitization to fungal allergens may be associated with respiratory allergic disease (RAD) and atopic dermatitis (AD). This study investigates the relationship between sensitization to different fungal allergens and the clinical manifestations of atopic disease. Methods: We retrospectively reviewed the medical records of atopic patients from the National Taiwan University Hospital from 2004 to 2009. A total of 133 atopic patients were found who were sensitive to at least 1 of the 3 most common fungi (Candida albicans, Aspergillus fumigatus, Penicillium chrysogenum) in Taiwan and were enrolled in the study. These patients were further divided into subgroups of isolated AD, isolated RAD and AD + RAD. The association between sensitization to fungi and allergic disease was analyzed by logistic regression analysis. Results: The sensitization rate to Candida-specific IgE was 81.2%, followed closely by Aspergillus at 69.2% and Penicillium at 63.2%. Isolated AD was the most common diagnosis. The levels of specific IgE antibodies against Aspergillus, Candida and Penicillium were highest in patients with isolated AD. Logistic regression revealed that isolated AD was highly associated with sensitization to Candida [odds ratio (OR) 10.45, 95% confidence interval (CI) 2.37–45.9]. In contrast, sensitization to Penicillium (OR 0.34, 95% CI 0.13–0.87)and Candida (OR 0.30, 95% CI 0.10–0.92) showed a negative association with isolated RAD. Conclusions: Fungal sensitization is more closely associated with AD than RAD. Our results suggest that specific sensitization to fungal allergensplays a critical role in the pathogenesis of atopic disease.