The presented research aims to evaluate highly energy-efficient dwellings, in particular Passive Houses (PH), in Flanders and in The Netherlands, based on end-user experiences. In the introduction the definition of PH in the Benelux countries Belgium and The Netherlands is compared with the Nordic countries and certification and comfort issues are discussed. The research is based on the results of questionnaires directed to owner-occupants and inhabitants of so-called Low-Energy, Passive and Zero-Energy Houses including different types of dwellings, such as single-family houses and apartments. The satisfaction levels of inhabitants have been investigated and evaluated regarding different comfort criteria. The research results for both countries have been compared with each other. They indicate that PHs in Belgium and in The Netherlands are generally well accepted by the inhabitants and perceived as comfortable. However, the perceived comfort can vary and some deficiencies need to be addressed to achieve high levels of comfort and user satisfaction in future PH projects. Particularly, summer comfort as well as the installation quality and user friendliness of current indoor climate systems can be improved. Additionally, the development of quality assurance schemes for PHs is discussed in this paper. Based on a comparison between the Dutch and the Flemish criteria, recommendations are given on items that are currently missing in PH certification and can lead to further improvement of building processes and national policy.