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Whereas the European Commission has long been regarded as the EU’s executive, the Council Secretariat has in recent years acquired siginificant executive powers of its own, in particular in the realm of EU foreign policy. In response to this development, there have been concerns about administrative fragmentation and rivalry and calls for the merger of the executive functions of the two institutions. Against this background, the article charts the relations between the Commission and the Council Secretariat across a range of shared tasks. It concludes that, despite an underlying tension induced by the provisions of the treaty, inter-institutional relations are largely co-operative. It provides a tentative explanation based on the expansion of EU institutions, the growing interconnectedness of EU policy-processes and the strengthening of a ‘supra-institutional’allegiance amongst EU officials.