Poultry is critical in fulfilling the protein requirements of the growing populations across the world. However, concerns about the public and environmental health impacts of bioaerosols emissions from intensive poultry facilities are increasing. In the present study, characterization of bioaerosols from air and litter samples was carried out using both culture and non-culture based methods (Flow cytometry). Eighteen controlled environment broiler houses (with approximate 27000 birds) were investigated and categorized into three groups on the basis of age: group I (1-20 days), group II (21-30 days) and group III (31-40 days). The air samples were collected on a polycarbonate filter using a volumetric pump at a height of 1.5 m both indoor and outdoor of the houses. The litter samples were collected from the floor in sterilized falcon tubes. An increase in the bacterial and fungal count was observed with the age of birds for both indoor air and litter samples. The bacteria found in the litter were reflected in the air but for fungal count, no such association was noticed. Outdoor air samples showed low microbial count as compared to indoor ones. Higher concentrations were recorded for the indoor and outdoor environment with the flow cytometry as compared to culture-based methods.