With the continuous improvement of the energy performance of buildings, ventilation plays a crucial role in the control of pollutants from indoor sources and related comfort and health effects. However, the ventilation system itself could possibly also be a source of indoor air pollutants such as microbial contaminants. Profound scientific and technical knowledge on the impact of the design, installation and maintenance on the real performances of ventilation systems is currently lacking. Therefore within a collaborative research project at the Belgian Building Research Institute (BBRI) the acoustic performance, energy consumption, air quality and ease of maintenance of five exhaust ventilation systems and twenty-eight balanced ventilation systems were evaluated in situ. Within this paper the results of the microbial analysis of the air quality part are presented. Different air sampling techniques were used to evaluate the supply and the indoor air in relation to the outdoor air. The impact of the accumulation and development of micro-organisms within the ventilation systems, especially in the ducts, the filters and if present on controllable supply grids, was also evaluated. The results indicate that the outdoor air quality has a major influence on the quality of the supplied and indoor air, especially for the mould load. However, human activity and the indoor environment tend to have a high impact on the indoor bacterial load. Exhaust ventilation systems were found to hardly alter the quality of the supplied air, leaving the indoor air microbial quality largely dependent on the outdoor air quality. In contrast balanced ventilation systems are capable of reducing the mould load, and to a lesser extend the bacterial load, of the supplied air. Filtration of the supplied air in the first place serves to protect the ventilation system from becoming dirtied. Nevertheless, the observed reduction in mould load of the supplied air within balanced ventilation systems can be regarded as an asset. However, the effectiveness of this filtration/protection was found to be largely dependent on the quality of the filters, filter housing (by-pass leakiness) and their state. These findings underscore the importance of a rational design, a proper installation and the importance of good maintenance.