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Small and medium sized enterprises represent a pool of economic dynamism and innovation of a country. Indeed, they are in the heart of the economy and induce an important source of knowledge and skills for centuries. If they want to survive, small and medium sized enterprises should establish a global protection from risk. However, in a highly competitive and globalized market, several questions arise about their future. Among these questions one major challenge is to know if they can protect their knowledge. This paper offers a methodology for threat analysis and assessment of vulnerability in the particular case of SMEs through the process of knowledge production.