The aim of this study was to characterize the association between phthalates exposure, through the representative biomarker, and childhood allergic and respiratory morbidity after adjusting for exposure to common indoor pollutants, especially bioaerosols. A total of 101 children were examined for their urinary metabolites of phthalates and indoor chemical or biological exposure. Children with higher urinary levels of phthalates are more likely to be categorized as "case" (aOR of MBzP=1.81, 95%CI=0.97-3.37), reporting higher frequency of parental reporting symptoms (aOR of MBzP=2.12, 95%CI=1.15-3.91), being found sensitized to inhalant (aOR of MBP=3.60, 95%CI=1.14-11.40) or mite allergens (aOR of MBP=2.48, 95%CI=1.34-4.62), and to present higher severity of physician-diagnosed diseases during clinic visits (β of MEHP=0.20, p=0.07). Moreover, I/O ratios of culturable fungi and endotoxin were also suggested as significant risks. The relative contribution from phthalates and indoor-originated bio-contaminants exposure on childhood allergic and respiratory morbidities is for the first time quantitatively characterized.