Both critical and optimistic claims have been made regarding the performance of heat recovery ventilation systems (HRVS) in dwellings. Such arguments are raised partly because two key aspects are not fully clarified, i.e. the performance criteria and the influence of uncertainties. In the current paper, an assessment method for HRVS considering the influence of uncertainties is described. This includes adequate assessment criteria, the method of identifying the uncertainties, and the method of addressing the influence of such uncertainties. The performance criteria consider the airflow performance, supply air quality and energy performance. Uncertainties in four aspects, including ventilation component, building properties, outdoor environment and occupant behaviour, are defined and related to five uncertainty sources ranging from the design phase to usage phase, i.e. design alternative, specification uncertainty, production deviation, modelling uncertainty and stochastic process. The estimation methods are given for each type of uncertainty based on the sources. Then, the method of carrying out the uncertainty analysis is introduced. This includes the calculation steps under a given commissioning status of the ventilation system, the uncertainty quantification techniques and the calculation steps. Afterwards, the method is applied to a case study of a counter flow heat recovery ventilation system in a reference Dutch house with the aid of simulations. Generally speaking, the method proposed in this article can provide an adequate framework for analysing or assessing the performance of HRVS in houses. As such it may contribute to a better understanding and a better design of this type of ventilation system.