The aim of this article is to present the model of innovation system in company, as well as the formulation of the concept of evaluation of the innovation capacity of enterprises. In this model will be presented the concept to analyze the relationship between the determinants of innovation organization and the level of innovation taking into account the variables mediating and regulating the established relationships. Determinants of innovation potential and ability determinants of innovation will be characterized such as competence of staff, modern infrastructure, cooperation in knowledge management, organization of work and the protection of knowledge (innovation) created within the organization. Using this concept of innovation the surveyed have been made in enterprises. The empirical part of the article will contain the results of the assessment of the degree of innovation of enterprises Malopolska Region. It was found that above all the knowledge and skills of employees of companies and cooperation between the actors of the industry is a highly innovative company. Emphasized at the impact of contextual variables in relation to innovation organizations drew attention to the size of the market, the nature of the organization, or the type of innovation.