Small and Medium-sized Enterprises (SMEs) are significant part of businesses in Slovakia. They participate in the creation of gross domestic product, export, import or other parameters of prosperity evaluation. Competitive fight is forcing businesses to bring new ideas, products or services to the market. Therefore, it is essential that SMEs should deal with innovations, which are considered as an essential part of business activities that contribute the development of competitiveness. SMEs can provide innovation activities at their own, in case that they have own funds. SMEs can use financial support from programs designed to support innovation. Another way to support the innovation in SMEs is the use of aid from supporting institutions. In Slovakia there are many institutions which support the sector of SMEs. The aim of the paper is to propose a single institution that would comprehensively support the sector of SMEs and would cooperate with other players.