AIM To investigate associations between both farm management factors and breed of dairy cow, and the incidence of farmer-observed clinical Johne's disease (JD) on dairy farms in four major dairying regions in the North Island of New Zealand. METHODS A questionnaire-based cross-sectional study was conducted to identify associations between both farm management practices and breed of dairy cow, and the incidence of clinical cases of JD suspected by farmers, on dairy farms in the Waikato, Taranaki, Wellington-Manawatu-Wanganui, and Wairarapa regions of New Zealand. Using multinomial logistic regression, the frequency of management practices was compared between farms on which no clinical cases of JD were observed, farms on which the observed incidence was low, and farms on which the observed incidence was high. RESULTS Of the 427 responding farmers, 201 (47%) had suspected clinical cases of JD in their herd in the preceding 5 years. Only 56/427 (13%) farmers observed an average annual incidence of >0.5 cases/100 cows during this period. Ninety percent (203/225) of farmers that had not observed clinical cases and 21% (42/201) of farmers that had observed clinical cases did not consider the disease a serious problem. Farmers and veterinarians had a moderate level of agreement regarding the JD status of a farm. Their perceptions were in agreement for 86% (38/44) of the high-incidence herds for which both a farmer's and a veterinarian's perception were available. The presence of Jersey cows in the herd and the purchase of bulls were most strongly associated with the incidence of clinical JD. Grazing calves in the hospital paddock, purchase of a large percentage of heifers, larger-than-average herds within our sample, and the use of induction were also positively associated with JD. Farmers who ensured heifers were at least 2 years old, rather than younger, when mixed with adult stock were likely to observe fewer cases of clinical JD. CONCLUSIONS AND CLINICAL RELEVANCE The annual incidence of farmer-observed clinical cases of JD was low, and the disease was generally regarded as of little importance by farmers. Farmers that had a high proportion of Jersey cows or that purchased bulls from either one or more than four sources were most likely to report clinical cases of JD. Management practices that could aid in the control of JD are the purchase of bulls free of JD, ensuring that calves do not graze in the hospital paddock, and ensuring that young stock are at least 2 years old prior to contact with adult stock.