In 2006, the Danish government decided to take new measures to control Salmonella and Campylobacter in Danish and imported retail meat. The legal basis for these new measures was article 14 in the EU food law, which states that food shall not be placed on the market if it is unsafe, among others, for reasons of contamination. This provision allows each member state to make a specific risk assessment of food batches, and decide whether a batch poses an unacceptable risk to the consumer or not. Here we present the basis for the risk assessment model on Campylobacter used in this new approach and the results of more than 3000 batches of broiler meat tested since 2007. The risk was assessed for batches with one or more samples positive for Campylobacter (>100 cfu/g). Reductions in the number of positive batches from 2007 to 2010 were observed for both domestic (from 17% to 7%, p = 0.01) and imported broiler meat (from 39% to 18%, p < 0.0001). During 2007–2010, only relatively few batches were deemed unsafe due to the presence of Campylobacter. The proportion of batches of domestic and imported broiler meat deemed unsafe varied from 0.3% to 1.0% for Danish broiler meat and from 0.2% to 7.7% for imported broiler meat. Still this initiative has been successful in significantly reducing the occurrence of Campylobacter in fresh meat available on the Danish retail market. To our knowledge, this is the first example of a risk based control system that enables quantitative day to day risk assessment of food batches. ► A risk based control system is presented. ► A quantitative case-by-case risk assessment model is developed. ► Case-by-case risk estimates of Campylobacter positive meat batches are presented. ► This initiative has reduced the Campylobacter occurrence in broiler meat.