Regional supply chains of quality products (PDO for example) build up their strategy on differentiation. The analysis by means of Transaction Cost Theory (Williamson, 1975, 1985) of two supply chains of Protected Designation of Origin allows us to identify the advantages and the disadvantages of organization forms for the transactions from milk producers to retailers. It was not possible to calculate the economies of costs linked to the observed governance mode. This is one of the classical criticisms of this approach. Nevertheless, the analysis remains interesting for us because it highlights the various mechanisms of the transactions at the different levels of the supply chain. We stress that the microeconomic character of the approach is a limit to the analysis. Mesoeconomic elements such as cultural bonds between the actors or macroecomomic elements such as market power of large retailers must be considered if we want to explain the encountered governance structures.