Energy-efficient buildings need mechanical ventilation. However, there are concerns that inadequate mechanical ventilation may lead to impaired indoor air quality. Using a semi-experimental field study, we investigated if exposure of occupants of two types of buildings (mechanical vs. natural ventilation) differs with regard to indoor air pollutants and climate factors. We investigated living and bedrooms in 123 buildings (62 highly energy-efficient and 61 conventional buildings) built in the years 2010 to 2012 in Austria (mainly Vienna and Lower Austria). Measurements of indoor parameters (climate, chemical pollutants and biological contaminants) were conducted twice. In total, more than 3000 measurements were performed. Almost all indoor air quality and room climate parameters showed significantly better results in mechanically ventilated homes compared to those relying on ventilation from open windows and/or doors. This study does not support the hypothesis that occupants in mechanically ventilated low energy houses are exposed to lower indoor air quality.