This article proposes a methodology to evaluate Technological Innovation Capabilities at university institutions, seeking to strengthen innovation management and advance in the integration of said institutions in the dynamics of the innovation system. The Triple Helix Model is adopted to analyze the relationships of university institutions with their surroundings. The proposal is conceptually built on a based on the perspective of resources and capabilities and on to the systemic congruence model of the organization. A fuzzy inference system is developed as the mathematical support of the evaluation process of the Technological Innovation Capabilties. The methodology is experimentally applied to a university institution in Medellín – Colombia, demonstrating its consistency, viability and practical usefulness.