Infrastructure refers to the fundamental facilities and systems serving a country, city, or area, including the services and facilities necessary for its economy to function. Infrastructure systems typically consist of interrelated constituent systems forming what is known as system of systems (SoS). 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 finding ways to address the consequences of unexpected events that often degrade the intended performance. This state of system 'wellbeing' will be referred as system integrity (SI). When applied to infrastructure systems this paper proposes a model suggesting that system integrity is a combination of operational performance, safety and resilience which become the set of criteria to assess SI. Each of these three factors is assessed by considering their specific 'key performance indicators' (KPI): Operational KPIs (KO), Safety KPIs (KS) and Resilience KPIs (KR). KOs could include KPIs for quality of service, reliability, availability, maintainability and cost; KSs could include KPIs for number and severity of accidents; and KRs could include KPIs for level of disruption and time for recovery to acceptable levels. In accordance with the proposed model system integrity can be defined as the "state of a system where it is performing its intended functions safely without being degraded or impaired by changes or disruptions in its internal or external environments". When the system achieves the state of perfect condition its system integrity is 100% or 1.0. Infrastructure systems may operate at lesser levels of system integrity (SI) and it is important to assess and monitor SI to make sure the system is operating within acceptable levels and to envisage ways to improve SI in the event of unexpected situations. The proposed model based on the on-going operational performance, safety and resilience of the each constituent system in the SoS is then developed into a method that applies the Analytic Hierarchy Process (AHP) (Saaty 1994) to create a quantitative assessment derived from qualitative and quantitative information. The method assumes that there is a set of KPIs for each of the agreed assessment criterion for operational performance, safety and resilience which were defined, agreed and can be individually assessed. The method uses qualitative experience-based information to weight the KPIs for each of the three criteria relatively to each other using AHP to obtain the overall assessment for operational performance, safety and resilience for each individual constituent system. These three criteria are also compared and weighted using the same approach to determine their level of contribution to SI which is then calculated using the actual value measured or estimated for each KPI. The method is then expanded to calculate the SI for SoS by applying the concept of 'supermatrix' proposed by AHP to address systems with feedback loops where individual components and assessment criteria influence each other. The SoS SI method is then applied into a hypothetical urban transport system for illustration purposes.