Musculoskeletal injury and disease are common in dogs, and a major cause of retirement in working dogs. Many livestock farmers rely on dogs for the effective running of their farms. However, the incidence of musculoskeletal disease has not been explored in working farm dogs. Here we explore the occurrence of musculoskeletal abnormalities in 323 working farm dogs that were enrolled in TeamMate, a longitudinal study of working farm dogs in New Zealand. All dogs were free of musculoskeletal abnormalities on enrolment to the study and were present for at least one follow-up examination. During the follow-up period, 184 dogs (57%, 95% confidence interval (CI) = 52%−62%) developed at least one musculoskeletal abnormality during 4,508 dog-months at risk, corresponding to 4.1 dogs (95% CI = 3.5-4.7) with recorded abnormalities per 100 dog-months at risk. The most common abnormalities were reduced range of motion and swelling of the carpus or stifle, while the hip was the most common site of pain. No major differences in incidence rate (IR) between sexes or types of dogs were observed, though Huntaways had a slightly lower rate of carpal abnormalities than Heading dogs (IR ratio = 0.6, 95% CI = 0.3-1.0). Eighty-one of 119 dogs (68%, 95% CI = 60%−76%) that had a first musculoskeletal abormality developed a second abnormality. The most common type of abnormality that was seen in the same dog more than once was reduced range of motion in the carpus (14 of 119 dogs, 12%, 95% CI = 6%−18%). Although we do not provide data on diagnoses, the high incidence rate of recorded musculoskeletal abnormalities and dogs' high activity mean it is likely that working farm dogs are at a high risk of conditions that could impair their welfare and reduce the lengths of their working careers. Preventing and managing musculoskeletal injury and illness should be a priority for owners and veterinarians caring for working farm dogs.