Background: Working farm dogs are invaluable on New Zealand sheep and beef farms. To date no study describing farm dog population and health has included information about incidence of illness and injury, or risk factors affecting health and career duration. This paper describes the methodology and initial results from TeamMate, a longitudinal study that was designed to address this gap. We describe the study population, husbandry practices, and prevalence of clinical abnormalities on enrolment. Methods: Data about the farms, owners, husbandry practices and dogs were collected on farm at approximately 6month intervals. All dogs over 18 months old and in full work were enrolled. Dogs were given physical examinations by veterinarians. On examination all abnormalities were noted, regardless of clinical significance. Results: Six hundred forty-one working farm dogs and 126 owners were enrolled from the South Island of New Zealand. Forty-nine percent of dogs were Heading dogs (314 of 641) and 48% Huntaways (308 of 641). Median age of dogs was 4 years (range 1.5-14) and median body condition score (BCS) was four on a 9-point scale (interquartile range (IQR) 3-5). Fifty-four percent of dogs were male (345 of 641), and 6% (41 of 641) were neutered. Eighty-one percent of owners (102 of 126) fed dogs commercial biscuits and meat sourced on farm. Forty-four percent of dogs (279 of 641) had bedding in their kennel, 14% (55 of 393) had insulated kennels, 69% (442 of 641) had been vaccinated and 33% (213 of 641) were insured. Clinical abnormalities were found in 74% of dogs (475 of 641). Common abnormalities involved the musculoskeletal system (43%, 273 of 641), skin (including scars and callouses; 42%, 272 of 641), and oral cavity (including worn and broken teeth; 35%, 227 of 641). Conclusions: Our results expand on those from previous surveys and indicate that musculoskeletal illness and injury, and skin trauma are the most commonly seen clinical abnormalities in working farm dogs. These results will provide a baseline for investigation of incidence and risk factors for illness, injury, retirement and death in New Zealand working farm dogs.