A nationwide cross-sectional study of 3335 employees was conducted in 320 offices in Japan to estimate the prevalence of building-related symptoms (BRSs) and determine the risk factors related to work environment, Indoor Air Quality, and occupational stress. Data were collected through self-administered questionnaires. The prevalences of general symptoms, eye irritation, and upper respiratory symptoms were 14.4%, 12.1%, and 8.9%, respectively. Multiple logistic regression analyses revealed that eye irritation was significantly associated with carpeting [odds ratio (OR), 1.73; 95% confidence interval (CI), 1.24-2.41], coldness perception (OR, 1.28; 95% CI, 1.13-1.45), and air dryness perception (OR, 1.61; 95% CI, 1.42-1.82). General symptoms were significantly associated with unpleasant odors (OR, 1.37; 95% CI, 1.13-1.65), amount of work (OR, 1.24; 95% CI, 1.06-1.45), and interpersonal conflicts (OR, 1.44; 95% CI, 1.23-1.69). Upper respiratory symptoms were significantly associated with crowded workspaces (OR, 1.36; 95% CI, 1.13-1.63), air dryness perception (OR, 2.07; 95% CI, 1.79-2.38), and reported dustiness on the floor (OR, 1.39; 95% CI, 1.16-1.67). Although psychosocial support is important to reduce and control BRSs, maintaining appropriate air-conditioning and a clean and uncrowded workspace is of equal importance.