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The concept of “Innovation” has changed considerably in recent years. According to new theories, the innovation emerges in a system of interrelated elements and determinants during which the idea changes to a commercialized output or process. The literature on the innovation has concentrated mainly on various aspects of innovation chain separately. In this paper we tried to investigate the general effects of the whole elements of the innovation chain simultaneously. These elements are: R&D expenditures, physical capital formation, human capital and patent filling (residence and non-residence). We utilized multivariable time-series methods including cointegration and vector error correction model (VECM) to assess the long-run effects of innovation elements on total factor productivity in Iran. Results show that excluding the human capital variable, other elements of innovation chain have positive effects on TFP among them, residence and non-residence patent filling having the normalized long-run coefficients of 0.58 and 0.48 respectively, are the most important factors affecting TFP in Iran.