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This paper aims to analyse the influence of structural characteristics and organizational determinants on the perception of obstacles to innovation in small developing countries. The study focuses on the interaction between these specific elements with important implications for both innovation policy and innovation management in the context of small emerging economies, which are generally characterized by financial and market constraints, weak institutional framework and low innovation performance. The empirical analysis is based on panel data of 5447 Ecuadorian firms from the National Survey of Innovation Activities for the periods 2009–2011 and 2012–2014. In contrast with the existing literature, which often analyses separately the influence of variables such as firm size or engagement in innovation activities on obstacles to innovation, this paper uses a nonlinear probability model to a better understanding …