In transition countries the firms’ size and equity property affect economic processes, including innovation activity in industry. Researche has shown that the key to accelerate economy development is technology transfer from foreign countries. Implementation of new solutions depends on medium and large organizations, rather than on the micro and small ones. Traditional micro and small regional enterprises feature a low level of capacity to take risk. An innovation activity in industry systems grows up over time, but only in small domestic enterprises, and it is similar to their foreign and larger competitors. This paper discusses the problems of size of enterprises and its impact on innovation activity in regional industry systems in West Pomeranian province in the period 2004–2006 and 2009–2011.