EU agencies have emerged as entities offering technical coordination to member states and support to the European Commission in different policy areas. Their expertise may play a role in responding to unexpected crises. Against this backdrop, we examine under which circumstances EU agencies, through their specialised expertise, are involved in transboundary crisis responses, and when they acquire a leading position in coordinating those responses. To do so, we study four agencies which faced crises: the EBA and the 2012 banking crisis; the ECDC and the 2014 Ebola outbreak; EFSA and the 2011 E. coli outbreak; and Frontex and the 2015 refugee crisis. Our findings discuss to what extent agencies' involvement in transboundary crises is related to functional (sector characteristics) and institutional (delegation of authority) variables. We also identify that under certain political conditions EU agencies' coordination capability is activated, allowing them to emerge as leading institutions in transboundary crises resolution.