This study investigated effects of physical exercise on musculoskeletal pain symptoms in all regions of the body, as well as on other musculoskeletal pain in association with neck pain. A single blind randomized controlled trial testing a one-year exercise intervention was performed among 549 office workers; specific neck/shoulder resistance training, all-round physical exercise, or a reference intervention. Pain symptoms were determined by questionnaire screening of twelve selected body regions. Case individuals were identified for each body region as those reporting pain intensities at baseline of 3 or more (scale of 0-9) during the last three months. For neck cases specifically, the additional number of pain regions was counted. Intensity of pain decreased significantly more in the neck, low back, right elbow and right hand in cases of the two exercise groups compared with the reference group (P<0.0001-0.05). The additional number of pain regions in neck cases decreased in the two exercise groups only (P<0.01-0.05). In individuals with no or minor pain at baseline, development of pain was minor in all three groups. In conclusion, both specific resistance training and all-round physical exercise for office workers caused better effects than a reference intervention in relieving musculoskeletal pain symptoms in exposed regions of the upper body.