We analyse industry–academic links in the context of a dual economy (or disarticulated industrial structure) in Ireland, a peripheral region of the EU. The duality found in the Irish industrial structure is the result of a FDI-led industrialisation strategy which has resulted in two distinct economic sectors – foreign and indigenous, respectively – with weak interactions between the two. Through increased public funding of academic research, the Irish government aimed to attract and embed new waves of higher-value foreign direct investment and increase the dynamism of its indigenous enterprise base. Based on a combination of quantitative and qualitative data, the paper analyses a crucial aspect of Ireland’s recent emphasis on STI policy – industry-academic linkages – and finds that the measures introduced reproduce in the public research system the uneven development found in Ireland’s productive system between indigenous industry and the foreign-owned industrial base.