The purpose of this thesis is to analyze empirically the relationship between market structure, measured by Herfindahl-Hershmann Index(HHI), and financial factors, and innovation in Korean industry panel datasets for 2000-2006. Results show that debt ratio and scale of the firm has a consistent positive effect on the investment in research and development. As more scale of the firm is getting bigger, the investment in R&D decrease. Also, as more debt ratio of firm rise, the investment for innovation increase. Concentration ratio, the HHI and the classification factor of High-tech industry and Low-tech industry has a consistent positive effect on the innovation. Factors affecting the investment in research and development include market structure and characteristics of industry as well as the internal affairs of the firm.