The indoor environmental quality and health of occupants in approximately 5000 dwellings were investigated by questionnaire covering the whole of Japan. The purpose of this survey was to clarify the association between indoor air quality and adverse health effects and to study effective ways of keeping indoor air clean using mechanical ventilation. Questionnaires were distributed to 7812 occupants living in mechanically ventilated houses across 47 Prefectures in Japan in February 2012 of which 5265 occupants replied. The contents of the 50-question survey addressed the indoor environment, installed equipment, the type of ventilation system, the pattern of operating space heating and mechanical ventilation, shelter performance of the building, occupants’ characteristics and health related quality of life (QOL) evaluated by using the Japanese version of the SF-8 method for measuring QOL. In this study, occupants’ adverse health effects based on health related QOL were positively associated with dampness. It is evident that control of indoor humidity levels and vapour condensation on the surface of building envelopes is necessary to reduce occupants’ health risk indoors. In addition, the risks for occurrence of visible vapour condensation and visible mould growth increased when the operating time of mechanical ventilation became shorter. Failures in operation and maintenance of a ventilation system may lead to dampness in buildings and the loss of occupants’ health.