Risk assessment in communities or regions typically relies on the determination of hazard scenarios and an evaluation of their impact on local systems and structures. One of the challenges of risk assessment for infrastructure operators is how to identify the most critical scenarios that are likely to represent unacceptable risks to such assets in a given time frame. This study develops a novel approach for prioritizing hazards for the risk assessment of infrastructure. Central to the proposed methodology is an expert elicitation technique termed paired comparison which is based on a formal mathematical technique for quantifying the range and variance in the judgements of a group of stakeholders. The methodology is applied here to identify and rank natural and operational hazard scenarios that could cause serious disruption or have disastrous effects to the infrastructure in the transnational Øresund region over a period of five years. The application highlighted substantial divergences of views among the stakeholders on identifying a single ‘most critical’ natural or operational hazard scenario. Despite these differences, it was possible to flag up certain cases as critical among the natural hazard scenarios, and others among the operational hazards.