Slaughterhouse work involves a high degree of repetitive and forceful upper limb movements and thus implies an elevated risk of work-related musculoskeletal disorders. High intensity strength training effectively rehabilitates musculoskeletal disorders among sedentary employees, but less is known about the effect among workers with repetitive and forceful work demands. Before performing randomized controlled trials it may be beneficial to assess the cross-sectional connection between exercise and musculoskeletal pain. We investigated the association between high intensity physical exercise and pain among 595 slaughterhouse workers in Denmark, Europe. Using logistic regression analyses, odds ratios for pain and work disability as a function of physical exercise, gender, age, BMI, smoking, and job position were estimated. The prevalence of pain in the neck, shoulder, elbow, and hand/wrist was 48%, 60%, 40%, and 52%, respectively. The odds for experiencing neck pain were significantly lower among slaughterhouse workers performing physical exercise (OR = 0.70, CI: 0.49-0.997), whereas the odds for pain in the shoulders, elbow, or hand/wrist were not associated with exercise. The present study can be used as general reference of pain in the neck and upper extremity among slaughterhouse workers. Future studies should investigate the effect of high intensity physical exercise on neck and upper limb pain in slaughterhouse workers.