This study aims to characterize levels of molds, bacteria, and environmental pollutants, identify the associations between indoor mold and dampness exposures and childhood allergic diseases, including asthma, allergic rhinitis, atopic dermatitis, using three different exposure assessment tools. A total of 50 children with their parents who registered in Seoul and Gyeonggi-do in Korea participated in this study. We collated the information on demographic and housing characteristics, environmental conditions, and lifestyle factors using the Korean version of the International Study of Asthma and Allergies in Childhood questionnaire. We also collected environmental monitoring samples of airborne molds and bacteria, total volatile organic compounds, formaldehyde, and particulate matter less than 10 µm. We evaluated and determined water damage, hidden dampness, and mold growth in dwellings using an infrared (IR) thermal camera and field inspection. Univariate and multivariate regression analyses were performed to evaluate the associations between prevalent allergic diseases and exposure to indoor mold and dampness. Indoor mold and bacterial levels were related to the presence of water damage in dwellings, and the mean levels of indoor molds (93.4 ± 73.5 CFU/m3) and bacteria (221.5 ± 124.2 CFU/m3) in water-damaged homes were significantly higher than those for molds (82.0 ± 58.7 CFU/m3) and for bacteria (152.7 ± 82.1 CFU/m3) in non-damaged dwellings (p < 0.05). The crude odds ratios (ORs) of atopic dermatitis were associated with < 6th floor (OR = 3.80), and higher indoor mold (OR = 6.42) and bacterial levels (OR = 6.00). The crude ORs of allergic diseases, defined as a group of cases who ever suffered from two out of three allergic diseases, e.g., asthma and allergic rhinitis, and allergic rhinitis were also increased by 3.8 and 9.3 times as large, respectively, with water damage (+) determined by IR camera (p < 0.05). The adjusted OR of allergic rhinitis was significantly elevated by 10.4 times in the water-damaged dwellings after adjusting age, sex, and secondhand smoke. Therefore, a longitudinal study is needed to characterize dominant mold species using DNA/RNA-based sequencing techniques and identify a causal relationship between mold exposure and allergic diseases in the future.