Several users of a newly built school building in a university (new building) complained about their deteriorating physical health. We measured the air quality in the new building, an old school building and atmosphere in September 2007 and February 2008. We also conducted a questionnaire survey of subjective symptoms of users in the new building in February 2008. The university administrator took some remedial actions to improve the indoor air quality after the first measurement. In September 2007, the concentrations of total volatile organic compounds (TVOCs) and 2-ethyl-1-hexanol in the new building were higher than those in the old building and atmosphere. Moreover, the concentrations of TVOCs exceeded the Japanese recommended guideline values. In February 2008, the concentrations of these substances in the new building were lower than the previous values. Out of the 177 users who were surveyed regarding subjective symptoms, 59 responded to the survey. In September 2007, 21 users felt that their physical health had deteriorated, while in February 2008, 12 users felt no deterioration. However, nine users still complained about the deterioration of their physical health. It was suggested that the improvement in the indoor air quality may be influenced by the decrease in room temperature. Even if the concentrations of VOCs are below the recommended guideline values, users with an enhanced sensitivity towards VOCs may lose their tolerance to low-level VOCs. Our findings suggested that a survey of the changes in the subjective symptoms of users should be conducted to evaluate the improvement in the indoor air quality of newly built buildings.