This article presents the results of a Dutch national study into performance of mechanical ventilation systems and its effect on the self-reported health and perceived indoor environmental quality of occupants. Ventilation systems with natural supply and mechanical exhaust ventilation (MEV) and balanced mechanical supply and exhaust systems with heat recovery (MVHR) were investigated. Surveys were performed in 299 homes, which included visual inspections and measurements of ventilation rates per room and installation noise levels. An additional survey regarding perceived indoor air quality and self-reported health was completed per household. Results show that shortcomings are common in many homes and for both MVHR and MEV. Shortcomings include insufficient ventilation rates, high noise levels, unclean systems and insufficient maintenance. The causes have been found to be related to failures during all the different stages of the building process, from design to use. The indoor environmental quality was perceived more positive in homes with MEV when considering air quality, perceived dryness of air, noise and control options. There was no clear relationship between self-reported health and shortcomings of ventilation systems. Some practical implications are presented to avoid shortcomings in future dwellings.