In order to improve the quality of ventilation systems, assessments are widely used. In this paper, 3 main assessment levels are distinguished based on the number of ventilation systems to be assessed and the assessment objective. The main assessment levels distinguished in this paper are global level (the assessment concerns a set of ventilation systems within a country or region), project level (the assessment concerns a set of ventilation projects within a housing project) and design level (the assessment concerns one ventilation system in a housing project for different environments and different types of occupants). Uncertainties should be considered and dealt with in assessments of domestic ventilation systems. The uncertainties that determine the in use performance of a domestic ventilation system are present in four aspects, ventilation components, building properties, outdoor environment and occupants. The structure of the uncertainties in an assessment is further studied starting from two types of uncertainties (reducible and irreducible) to two levels of uncertainty data (basic level and mixed level data). Two different methods how to deal with different assessment levels and their uncertainties are subsequently discussed as well as how to choose a method for a specific assessment level. The methods that are developed are the accurate method and the prototype method. Finally, a brief demonstration of the described concepts and methods is given.