We describe the paratuberculosis management practices applied in dairy herds in the Netherlands. The findings from paratuberculosis seronegative and seropositive herds were compared to discover possible risk factors. In total, 370 randomly selected herds with ≥20 dairy cows were surveyed. A questionnaire was used to collect data on current and previous paratuberculosis management practices. All cattle aged ≥3 years were serologically tested for paratuberculosis using an enzyme-linked immunosorbent assay. Herds with >33 tested cattle, of which only one was seropositive, were excluded to reduce the risk of including false-positive herds in the analysis. A comparison of the management data of the seronegative herds (n = 166) and the seropositive herds (n = 143) showed that in both groups important management measures for the prevention of paratuberculosis, such as calving in a cleaned calving area, removing the calf immediately after birth, and feeding paratuberculosis non-suspect roughage to calves, were used only rarely. However, such measures should be regarded as the critical first step to control the disease and/or reduce its prevalence. Using univariable analysis, four factors were statistically different between seronegative and seropositive herds: herd size, cows with clinical signs of paratuberculosis, prompt selling of clinically diseased cattle and feeding milk replacer. Using a multivariable logistic regression model, only herd size was a significantly different factor. These results indicate that most of the paratuberculosis preventive management measures were executed on these Dutch dairy farms only to a limited extent.