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A cross-sectional study using a modified Nordic musculoskeletal questionnaire asked 867 New Zealand veterinarians about the presence or absence of musculoskeletal discomfort (MSD). Participants were asked if MSD affected their normal activities and if it required any period(s) of absence from work. Additional questions enquired about work activities, psychosocial factors and workload. A binary logistic regression analysis was used to quantify the association between identified risk factors and the presence of MSD requiring absence from work in the previous 12 months, controlling for the presence of known confounders. The overall period prevalence of MSD was 96%, 67% had normal activities being affected and 18% of participants reported that they had been absent from work due to MSD. The lower back was the body site most commonly reported for MSD (73%). Factors increasing the odds of MSD requiring time off work for clinical veterinarians were 10 year increases in age (OR 1.26, 95% CI 1.05-1.52), work involving awkward grip and hand movements 100% of time (OR 12.91, 95% CI 3.46-4.21) and those who were dissatisfied with the level and difficulty of their work (OR 2.27, 95% CI 1.11-6.56). These findings have implications for health, lifestyle and retention rates for veterinarians.