Increasing environmental awareness has led to new, energy-efficient building standards such as the German Passivhaus-standard. This study was designed to investigate the indoor air quality (IAQ) of four different Dutch low-energy houses built according to this standard. Air flow, indoor air pollutants (CO2, CO, H2CO), temperature (T), and relative humidity (RH) were measured over a period of several weeks. The residents kept a logbook of activities and filled in a questionnaire regarding use of the facilities. In some cases, wrong usage of the ventilation system resulted in high levels of CO2. Average airflow in use was in all cases lower than recommended by the Dutch Building Code while the capacity installed is proficient. The use and application of mechanical ventilation systems in low-energy houses is the bottleneck for creating an acceptable level of IAQ. Residents should be educated in its use and extra attention should be paid during installation.