The indoor air quality in public buildings is essential for the health of employees and visitors. To investigate the potential influence of airborne germ loads on human health, two sampling campaigns were conducted during 2009 in several public buildings in Timisoara (Romania). The quality of air revealed highly significant differences among different sites. Cluster analysis accurately classified the investigated buildings into three main groups and for most groups of aerial microorganisms, the measured values rarely fell below the normal concentrations in indoor environments. Although the structure of airborne flora varied widely among different locations, mesophilic bacteria and molds were the main determinants of indoor air quality in investigated buildings. It was found that these two factors explained over 90% of the overall average dissimilarity in the structure of indoor airborne microbiota. Moreover, multivariate analysis showed a strong positive relationship between these two factors, which is probably related to the number of daily occupants and visitors as well as to the building age. Further research is required to determine more accurately the relationship between ventilation performance and air quality.