Paratuberculosis is a chronic infection of economic importance to the cattle industry and a voluntary control programme is offered to Danish dairy farmers. Our objective was to evaluate spatial differences in both control programme participation and paratuberculosis prevalence in Denmark. The study included 4414 dairy herds: 1249 were participating in the control programme, and 1503 were tested for antibodies to Mycobacterium avium subsp. paratuberculosis (MAP). Spatial differences were evaluated by kernel smoothing, kriging, and cluster analysis. Participation was lowest among herds on the island Zealand (≤23%). The risk of a herd being infected with MAP was found to be high on most of Zealand, but the uncertainty of this result was large due to a limited number of tested herds. In the rest of the country, the south western part of the peninsula Jutland had the highest risk of MAP (≥91%). The risk of MAP was also high (86-91%) in the northern part of both Jutland and Funen. The predicted apparent within-herd prevalence was highest (5-8.5%) in some local areas across Jutland, in the north western part of the island Funen, and in the south and western part of Zealand. Scan statistics located the primary cluster of herds with high apparent within-herd prevalence in the western part of Funen. Furthermore, a number of significant clusters were found in Jutland and a single significant cluster in Zealand. Consistency was found between kriging and scan statistics results with respect to location of areas with high apparent within-herd prevalence of MAP. Potential explanations for differences in participation include herd size and local herd health advisers, whereas for example soil characteristics might influence prevalence. Further studies are needed to evaluate these and other risk factors.