The article deals with identifying the obstacles to the commercialization of academic research results generated by the differences in institutional environment for the production of scientific knowledge and the production of technological products by innovative start-ups. To do this, it gives the characteristics of the above-mentioned institutional environments, as well as patterns of behavior in them that do not have the character of formal or informal institutions. Particular attention is paid to psychological traits of entrepreneurs and their cognitive abilities, which may not be available to teachers and researchers at universities and research organizations. Comparison of the content of these environments gives grounds for distinguishing two types of institutional barriers: the first one is of a general economic nature and can generate significant costs for the work of innovative start-ups; the second one is intra-organizational in nature and can generate high risks of transition from science to commercial industry, preventing researchers and teachers from making decisions about creating innovative technology start-ups. The paper concludes with recommendations to reduce the level of barriers of the second type. In particular, to compensate for the risks associated with possible consequences of failure to create a startup and the difficulties of returning to the field of research activity, university management could legally guarantee a teacher or researcher a return to work in scientific or educational departments of faculties for at least five years after creating a startup.