The Small and Medium-Sized Enterprises (SMEs) are a necessary element of the social and economic development of the national economy from the perspective of their significant contribution to employment, innovative capacity, and flexibility. Innovative SMEs are necessary building block in the restructuring of transition economies. The successful reformers of the Central and Eastern Europe countries can promote policies conducive to the development of innovative SMEs, and consequently benefit from the economic advantages of SMEs. However, the majority of the Commonwealth of Independent States (CIS) countries are lagging behind significantly. This paper gives the analytical description of the development of SMEs in post-socialist countries during the transition process within the framework of the market reforms. The main barriers to growth of SMEs with innovation capacity are the institutional environment, and the inadequate attitude of the government towards small companies. The countries which integrated to European Union been able to overcome these barriers considerably, while the CIS countries do not have a record of significant achievement in this area.