The presence of micro-organisms in air is taken for granted, but understanding the identities, distribution and abundance of airborne micro-organisms remains in its infancy. Indoor exposure to micro-organisms has been related to range of adverse health outcomes. The indoor levels of particulate matter and bioaerosols were monitored in thirty houses across Lahore, Pakistan. Two DustTrak aerosol monitors (model 8520, TSI Inc.) were run simultaneously in the kitchens and living rooms of the selected sites to measure fine particulate matter. At the same time, agar coated petri plates were exposed face upwards for twenty minutes to sample the micro-organisms present in surrounding air of both micro-environments. A total of 7 bacterial species and 11 fungal species were identified including Staphylococcus spp., Bacillus spp., Micrococcus spp. and Serratia spp. while the predominant fungal species were Alternaria alternata and Aspergillus spp. The concentrations (cfu m–3) for bacteria ranged from 472 to 9829 in the kitchens and from 275 to 14469 in the living rooms. Likewise, the fungal cfu m–3 ranged between 236 and 1887 in the kitchen and from 315 to 1887 in the living room. A seasonal variation in bioaerosols was evident in the kitchens while being not so pronounced in the living rooms. A linear regression model showed a direct association of temperature with bacteria and fine particulate matter but not with fungi. Ventilation was also observed to have a significant impact upon PM levels. Out of 30 households sixteen had the presence of at least one individual with allergenic reactions. These findings highlight the enhanced risk of exposure to fine particulate matter as well as bioaerosols in the urban residential built environment in Pakistan.