The present paper assesses the effect of the formation of cluster organisations on the innovation performance of member enterprises in two different industries – the traditional textile manufacturing industry and the new nanotechnology industry. Innovation performance is explored using Data Envelopment Analysis in two phases. In the first phase, it examines the ability of enterprises to transform resources (labour force, long-term capital, intellectual capital) into registered industrial property rights: patents, utility models, industrial designs, and trademarks. In the second phase, it assesses the ability of enterprises to commercialise industrial property rights and generate profits. Innovation performance then integrates both phases. In each industry, two samples were assessed: member enterprises of cluster organisations, and enterprises that operate in the same industry and region but are not members of a cluster organisation. The results of the research show that the existence of a cluster organisation has a greater effect on innovation performance in the traditional textile manufacturing industry. In contrast, in the new nanotechnology industry, the existence of a cluster organisation did not prove to have any significant effect on innovation effectiveness. In this industry, the existence of a cluster organisation had only a partial effect related to better industrial property rights commercialisation. Research shows that the type of industry is an important factor in the innovation performance of clustered enterprises.