The study objectives were: 1) to assess which cow characteristics were associated with the temporal repeatability of a positive Johne's disease (JD) milk ELISA result in dairy cows, 2) to investigate the association among JD milk ELISA positivity, breed, milk production and risk of removal, and 3) to evaluate the risk assessment (RA)-based JD control program implemented in Ontario and western Canada between 2005 and 2009. The first two objectives were addressed using the results of all JD milk ELISAs (n = 85,135) conducted by CanWest Dairy Herd Improvement between 2005 and 2009 and associated milk production records for those cows. The third objective was addressed using the RA and milk test data from 238 Ontario and western Canadian herds, participating in a voluntarily JD control program between 2005 and 2009. The higher the milk production and the optical density (OD) of the initial positive JD milk ELISA, the less likely the cow was to change her JD test status at a subsequent test. Cows of Channel Island breeds were more likely to test positive with the JD milk ELISA than all other breeds. Test-positive cows produced, on average, less milk than test-negative herd mates in the lactation they were tested, and the differences in yield increased with OD score and parity of the cows. Additionally, the higher the OD score of milk ELISA-positive cows, the higher their risk of being culled compared to test-negative herd mates. Producers enrolled in the JD control program generally liked it and implemented, on average, 2 of 6 recommendations, which was associated with decreased RA scores. The initial RA scores were not associated with the JD test-status or prevalence of test-positive cows at the follow-up herd test. However, risk factors for the herd-positivity and for an increasing number of test-positive cows included: the presence of test-positive and clinical JD cows in the herd in previous years and the feeding of pooled colostrum to newborn calves. Feeding of monensin to young animals was associated with a decrease in the proportion of observed JD test-positive cows on the farm.