Dynamic economy needs efficient human capital which includes elites, professionals and entrepreneurs to continue innovation and competitiveness. Brain drain in the developing countries leads to growing gaps between innovation and technology in country of origin and destination. Therefore this study is investigated the effect of brain drain on innovation in countries of the middle east region and the U.S.A during period of 2000-2009. The results showed that the Islamic Republic of Iran among the region countries has taken first rank in terms of brain drain, also in terms of innovation product has a big gap with the U.S.A. It should be noted Iran in comparison with other region countries potentially is relatively well in terms of indicators of innovation,. Middle east countries also have significant differences with the United States in terms of innovation. On the other hand countries such as Turkey and Kuwait, have less brain drain than other region countries, also have relatively good position in terms of innovation indicators.