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The relationship between financial and real sectors of economy has been considered in various economic studies. This paper investigates the effect of financial system structure on economic growth using Dynamic Panel method (GMM) for 39 countries during 2000-2009. The estimation results show that financial structure has no significant effect on economic growth in both the entire set and developed countries, while this effect is significant in developing and emerging countries. In other words, real sector performance in market-based financial system is better than bank-based financial system in developing and emerging countries. In addition, financial development has significant and positive effect on economic growth in entire set of countries, and this effect is higher in developing and emerging countries than developed countries.