The main purpose of this paper is to investigate the effect of market structure on innovation and R&D in Iran’s manufacturing sector. To do this, first, statistical data for Iran’s manufacturing sector has been gathered in International Standard Industrial Classification (ISIC) format, then mutual effects of concentration, innovation and R&D, advertising and profitability in different industrial activities have been analyzed using simultaneous equations system and Error Component Tow Stage Least Squares (EC2SLS) during 1996-2007. The results show that industrial concentration has a significant and inverted U-shaped relationship with innovation and R&D. In addition, R&D expenditure declines with increases in profitability. The investigation of the factors affecting manufacturing structure indicates that although innovation and R&D has no effect on manufacturing structure, but profitability and performance of top firms affect their concentration. Our findings exhibit the ineffectiveness of concentration and innovational behavior on industries performance; whereas increasing market concentration results in advertising expenses and innovational behavior of firms raises advertising expenses. Similarly, the lagged and accumulated effects of R&D confirm the existence of an inverted U-shaped relationship between concentration and R&D

Keywords: market structure, competition, Behavior, Market performance, Research and Development, Concentration, Profitability, efficiency, Advertising, Manufacturing Sector, Simultaneous Equation System, Error Component Tow Stage Least Squares

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