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This study aimed to examine a detailed breakdown of costs (absenteeism, presenteeism, and medical/pharmaceutical expenses), of the employees in four pharmaceutical companies in Japan.This is a cross-sectional study. Absenteeism and presenteeism were measured by a self-administered questionnaire for workers, and their costs were estimated using the human capital approach. Presenteeism was evaluated by the degree affected quality and quantity of work. Medical and pharmaceutical expenses were obtained by insurance claims.The monetary value due to absenteeism was $520 per person per year (11%), that of presenteeism was $3055 (64%), and medical/pharmaceutical expenses were $1165 (25%). Two of the highest total cost burdens from chronic illness were related to mental (behavioral) health conditions and musculoskeletal disorders.A total cost approach can help employers set priorities for occupational health, safety, and population health management initiatives.