Investigation was conducted with the aim to get insight into the perception of different barriers for implementation of innovation projects by the employees in the companies in Serbia in dependence of employees' educational level, their perception of companies' innovativeness and the ownership structure of the company. Questionnaire-based research of perception of risk, finance, employees, management, social environment and information related barriers was carried out in the companies with different ownership structure: public enterprises, subsidiaries of multinational companies and companies owned by domestic entrepreneurs. In addition to the company's ownership, respondent's education level and perception of company's innovativeness were used as independent variables. The hypothesis that the perception of the barriers to the implementation of innovative projects in companies in Serbia by employees depends on the level of their education was not supported while the other two hypotheses stating that perception of the barriers to innovation projects depends on employee's perception of company's innovativeness and the ownership of the company were both supported. High level of perception of barriers in Serbia imposes the limitations to the implementation of innovation projects in Serbia, and thus case-specific activities aimed at overcoming of barriers to innovation projects should be planned and implemented.