Background: In recent years, the epithelial barrier hypothesis has been emphasized in the formation of allergic diseases. Transepidermal water loss (TEWL) occurs through diffusion and evaporation from the skin to the external environment. There are few studies on TEWL in allergic diseases. Objective: This study evaluated the relationship between patients with atopic diseases and healthy controls and hygiene habits in TEWL. Methods: The study was conducted on patients who were followed up for atopic disease (asthma, allergic rhinitis, immunoglobulin E mediated food allergy, and atopic dermatitis) and healthy children. TEWL measurement was in a room that was stable in terms of humidity and temperature by using a widely validated open room system. During the measurement, the participants reported their frequency of taking a shower and cleaning product use. Results: In the study group, TEWL was measured in 182 patients, and the median (min-max) TEWL was 21.3 g/hm² (7.8-101.3 g/hm²) in the disease group and 9.6 g/hm2 (3.9-30.3 g/hm²) in the control group (p < 0.001). The number of weekly baths was higher in the disease group (p < 0.001). The cutoff for atopic diseases was 13.2 g/hm² (sensitivity, 83.2%; specificity, 84.3%; p < 0.001). Conclusion: High TEWL in atopic diseases supports the epithelial barrier hypothesis associated with disease development. Further studies are necessary to determine the threshold between healthy controls and the patients in the disease group. The TEWL measurement can be an effective method to determine the risk groups. Moreover, further studies related to factors on TEWL and treatment methods to reduce this loss are necessary, too.