Infrastructure systems typically consist of technical structures comprising of physical and operational components of interrelated constituent systems forming what is now known as system of systems (SOS). The complexity and uncertainty of unforeseen events that are inherent characteristic of infrastructure systems makes it impossible to predict undesirable emergent behaviours that could push the operation of such systems away from their intended purposes. Infrastructure systems present numerous challenges throughout their lifecycles. This paper addresses one of these challenges that is presented during operation, when managers need to report 'how well' the system is performing and find ways to address the consequences of unexpected events that often degrade the intended performance. This paper adopts a definition of system integrity (SI) to assess the SI for each constituent system and then combines them into the overall SI for the SoS. The proposed method is based on the on-going operational performance, safety and resilience of the constituent systems and applies the Analytic Hierarchy Process (AHP) to create a quantitative value derived from experience-based qualitative assessment. In this method, firstly the key performance indicators (KPI) for each of the agreed assessment criteria for operational performance, safety and resilience are defined and individually assessed. Then the KPIs for each of the three criteria are weighted relatively to each other to obtain the overall assessment for operational performance, safety and resilience for each individual system. These three criteria are also compared and weighted to determine their level of contribution to the SI for the system which is then calculated. The method is then expanded to assess SI for SoS and applied into a hypothetical urban transport system for illustration purposes.