The objective of this prospective cohort study was to evaluate if peak or cumulative musculoskeletal discomfort may predict future low-back, neck or shoulder pain among symptom-free workers. At baseline, discomfort per body region was rated on a 10-point scale six times during a working day. Questionnaires on pain were sent out three times during follow-up. Peak discomfort was defined as a discomfort level of 2 at least once during a day; cumulative discomfort was defined as the sum of discomfort during the day. Reference workers reported a rating of zero at each measurement. Peak discomfort was a predictor of low-back pain (relative risk (RR) 1.79), neck pain (RR 2.56), right or left shoulder pain (RR 1.91 and 1.90). Cumulative discomfort predicted neck pain (RR 2.35), right or left shoulder pain (RR 2.45 and 1.64). These results suggest that both peak and cumulative discomfort could predict future musculoskeletal pain.