Indoor microbial exposure has been implicated in various adverse health effects. This study aimed to examine the effects of ventilation efficiency on indoor/outdoor (I/O) levels of airborne microbes in homes with natural ventilation, a predominant type adopted by most residential buildings in Taiwan where high microbial concentrations have been reported. Environmental investigations were conducted in 44 homes. Indoor and outdoor airborne bacteria and fungi were collected using a Burkard sampler with Trypticase Soy agar and Malt Extract agar in a flow rate of 10 L/min. Air change rate (AC/H) was measured using the tracer gas concentration decay method. Indoor airborne bacteria and total fungi levels in most investigated houses were generally greater than 1000 CFU/m3. The most frequently isolated fungal genera were Aspergillus, Penicillium, Cladosporium, Alternaria and Yeast. Only the I/O ratios of A. niger and Penicillium were significantly higher for those homes with an air change rate of less than 2.13/h, the median value, compared to those with greater than 2.13 (p<0.05). A weak, but not significant, association was observed between the increasing I/O ratios of Cladosporium and Alternaria and increasing ACH rates. Such an association, however, could not be identified with concentrations of indoor and outdoor airborne bacteria. Results also suggested higher air change rate in residences with natural ventilation may, in turn, elevate effectively indoor microbial levels of outdoor origin for there may be absence of proper filtration.