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The article explores the implications of the smart specialisation approach on core-periphery relations in Estonia and Slovakia. Despite accounting for one-third of the entire EU budget, Cohesion Policy has produced only modest results in achieving its goal of territorial cohesion between centres and peripheries. This raises the question of the role of Cohesion Policy's current approach—smart specialisation. By applying the analytical concept of peripheralisation, the article examines how the formulation and implementation of smart specialisation is governed in Estonia and Slovakia, both of which are characterised by large territorial disparities between the capital region and the rest of the country in terms of socio-economic development and participation in decision-making. Specifically, the article explores how the smart specialisation approach is interpreted domestically in terms of strategy formulation, priority-setting and spatial targeting of measures, and whether the particular domestic interpretation of smart specialisation acknowledges the unequal economic and research and innovation potential as well as different institutional capacities of central and peripheral regions. Drawing on extensive document analysis and 20 expert interviews with policy-makers and stakeholders in Estonia and Slovakia, it is argued that while ambitiously promoting an approach of 'inclusive growth' for the benefit of all regions, the influence of smart specialisation on core-periphery relations shows to be ambiguous. Fuzzy priority-setting, a lack of strategic and administrative capacities at the regional level and inhibiting policy-making routines discourage and, at times, prevent such a demanding approach. The article concludes that smart specialisation in its current form does not benefit central and peripheral regions equally. Rather, its demands in terms of formulation and implementation are likely to reinforce the disparities between those regions with capacities to handle such an ambitious approach and those regions without such capacities. [ABSTRACT FROM AUTHOR]