In this clinical trial, 3 commercial dairy herds vaccinated every other heifer calf against Johne's disease using a conditionally licensed commercial vaccine until two cohorts with the greater of the following were obtained: 10% of the adult herd or 50 head per cohort. Each herd participated in an annual Johne's disease risk assessment and herd management plan and had made efforts to reduce the risk of Johne's disease transmission prior to initiating this project. Baseline prevalence estimates indicated that the three herds were moderately to heavily infected with Johne's disease. Fecal samples from heifers from the cohort groups were collected at first calving and at the 90 day pregnancy check at each subsequent lactation and tested using bacterial culture with liquid media. After at least one test per cohort cattle, heifers from the vaccinated cohort had significantly fewer positive fecal cultures than the non-vaccinated cohort (relative risk 0.32; p value < 0.01). The concentration of fecal shedding and clinical disease, although not statistically significant at this point of the study, both showed a trend toward lower levels of fecal shedding in vaccinated cohorts as compared to the non-vaccinated cohorts. These preliminary data suggest a protective role for Johne's disease vaccine in combination with management changes in moderate to heavily infected herds.