We conducted a longitudinal epidemiological study for over 1year in Tokyo and Osaka, Japan, beginning June 2015, to examine the association between indoor environmental factors and building-related symptoms (BRSs) in office workers. Data were obtained from 483 subjects (225 females and 258 males) in 24 office rooms in 11 office buildings. Environmental monitoring was conducted for hygro-thermal conditions and carbon dioxide and sampling was performed for indoor air pollutants. Questionnaires were concurrently administered to collect information on participants' perceptions of their comfort and health and the conditions of the work environments. Multivariable analyses revealed that upper respiratory symptoms were significantly correlated with a decrease in both relative [odds ratio (OR): 0.77; 95% confidence intervals (CI): 0.62-0.95; p=0.014] and absolute humidity (OR: 0.89; 95% CI: 0.81-0.97; p=0.008). Statistically, significant evidence was found that average relative humidity of <38% (OR: 2.68; 95% CI: 1.36-5.27; p=0.004) showed the most significant association with increased risk of upper respiratory symptoms. Air concentrations of carbon dioxide showed no significant correlation with BRSs at mean concentrations <1000 ppm in most buildings surveyed. Most indoor air pollutant concentrations were relatively low or lower than the values set by indoor air quality guidelines and the values of thresholds for sensory irritation. Air concentrations of indoor air pollutants showed no significant correlation with BRSs. Our data emphasize the importance of appropriate humidity control during low humidity in winter.