Critical infrastructure systems (CISs) play an essential role in modern society, as they are important for maintaining critical social functions, economic organisation, and national defence. Recently, CISs resilience has gained popularity in both academic and policy filed facing increased natural or technological disasters. Resilience assessments have become convenient and common tools for disaster management, as assessment results provide useful information to CIS managers. However, CISs resilience assessment is facing challenges of being practical to use in operational risk management. Although there are many existing assessments for CISs resilience, some shortcomings relating to assessment criteria, which cannot turn resilience useful in practical operation, are frequent in their assessment process. Existing assessments are based on different definitions, which makes criteria generalization difficult. Besides, these assessments are not comprehensive enough. Especially, few assessments address both the cost, effectiveness, and safety of optimisation actions. Moreover, most of the suggested criteria are not specific enough for being used for practical CISs risk management in real cases. This article develops therefore a multi-criteria framework (MCF) for CISs resilience, consisting of general criteria and a guide for defining specific sub-criteria. In this MCF, the side effects, cascading effects and costbenefit in resilience scenarios are considered indispensable for CISs resilience assessment. The paper also presents an example of the application of the developed guide through two detailed scenarios, one on a single infrastructural system affected by a natural disaster, and the other addressing the interdependence of this infrastructural system and an urban healthcare system. The designed MCF contributes to the operationalisation and comprehensiveness of CISs resilience assessments.