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The goal of the paper is to analyse the potential for the innovation of cross border clusters from the sector of agriculture. The methodology which is used is the research of intellectual property (IP) of the clusters' members and clusters by using a specific questionnaire for clusters in two countries: Hungary and Serbia. The analysis of results shows a high level of innovativeness within the clusters' members and the need of protection of their intellectual achievements. The similar results were achieved in both countries. They show that the IP rights at the level of clusters should be protected as the cross border trademark and the name of origin. The scientific contribution of this paper is to introduce the concept of the joint cross border IP protection for two or more clusters from different countries which might be applied across the EU.