There is a lot of competition on the market. Therefore companies are trying to motivate to make progress and develop new things - innovations. Innovation ensures success and long-term competitiveness in the market. However, it is essential to protect them and one of the tools to protect intellectual property for innovation is the trademark that we will focus on in this work. In this work we analyze the use of trademarks in Slovakia as a tool to protect innovations representing the output of the innovation process. In the theoretical part, we discuss the issues of innovation, innovation process and protection of intellectual property from the perspective of different ways of protecting innovations. In analytical part, we focus specifically on the trademark, as one of the tools for protecting intellectual property of innovations, from the perspective of its use in Slovakia, the EU and other aspects. From this analysis, we can note the low use of trademarks as tools to protect innovations in Slovakia.