The effective knowledge transfer and innovation activities in the agri-food supply chain may push all producers in the vertical to improve their competitiveness while saving resources. In the paper the innovation activities and knowledge transfer in the dairy value chain in the Czech Republic are examined in order to assess the potential for enhancing sustainable dairy production. A particular attention is given to the collaboration with R&D organisations and other important agents. Concurrently the role of the structural changes is considered. The methodological approach builds on the concept of the sectoral system of innovation. Based on statistical figures and face to face interviews the increasing dynamics in the innovation process is observed, however, farmers and processors are in their innovation activities disconnected and their collaboration with research institutions and other companies is rather low. The main innovation objectives as well as drivers and barriers of the collaboration are specified.