EU agencies within the EU Agency Network for Scientific Advice (EU ANSA) provide scientific advice to EU policy makers across a broad spectrum of disciplines from public health to gender equality. The primary role of the EU agencies in ANSA is to collect, use and communicate scientific evidence, and hence there is an onus to identify and communicate the inherent uncertainty that is intrinsic to the scientific process. Doing so ensures that policy makers better understand the strength of the evidence base presented, and that resulting policy is made on the basis of fully informed choice. This study presents a preliminary exploration of approaches taken by EU ANSA members to address scientific uncertainty in their scientific outputs. It aims to provide a basis to identify common themes and issues, and stimulate further thinking about the definition, identification and communication of scientific uncertainty in scientific advice outputs from the agencies. The methodology involved development of a simple framework to assess; a) overarching guidance on handling uncertainty in each agency, and b) specific scientific outputs from each agency to understand how uncertainty was handled’ ‘in practice’. Participating agencies were also invited to submit pertinent examples of scientific outputs which illustrate good practice and challenges in handling scientific uncertainty.