We investigated the prevalence of musculoskeletal disorders (MSD) and skin disease within a Japanese compact disk (CD) manufacturing plant. For this study, a stratified cross-section of workers completed self-reported questionnaires distributed over a 6-month time period. Low back pain (LBP) was the most commonly reported category (affecting 20.1%), followed by MSD of the shoulder (15.4%), neck (10.1%) and head (5.4%). Dermatitis was the most frequent skin disease (affecting 8.1%), followed by eczema (3.4%), acne (3.4%) and xerosis (2.7%). The odds of suffering neck MSD was 10.8 times higher among staff who sat in a chair all day (95% CI 1.8-112.8, P < 0.05). Standing all day was also a risk factor for this condition (OR 8.2, 95% CI 1.2-81.7, P < 0.05). Female gender increased the risk of shoulder MSD 4.3 fold (95% CI 1.4-13.7, P < 0.05), as did alcohol consumption (OR 3.3, 95% CI 1.1-11.9, P < 0.05). The odds of suffering any skin disease were significantly enhanced by working longer than 12 months in one's current job (OR 10.7, 95% CI 1.5-7.3, P < 0.05) and having a history of atopic disease (OR 7.2, 95% CI 2.6-21.4, P < 0.001). Overall, the staff within our study reported generally lower levels of MSD and skin disease than in previous investigations of other workplaces.