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Background  Patient portal use can be a stimulant for patient engagement. Yet, the heterogeneous landscape of tethered patient portals, is a major barrier to further portal development and implementation. A variety in portal access means, functionalities, usability and usefulness exists; without having accurate sight on patient perspectives. We aimed to get insights on possible coherence between patients’ preferred usage factors of portals and patients’ prioritization of functionalities, within the complexity of their disease management across different healthcare organizations.    Methods  A conjoint analysis questionnaire was sent to patient panels of two large patient associations in The Netherlands, centered on heart and vascular diseases and lung diseases.    Results  Of 1294 patient respondents, 81% were 55+ years old and 49% were 65+ years old. Overall respondents significantly prioritized user-friendly access to a portal, via a laptop or desktop. Patients aged < 65 were less negative about using tablets to access a portal compared to the total respondents. Patients had no preference for a digital interoperable export functionality; most respondents preferred to create printable overviews. Built-in publication delay of two weeks for medical information was not preferred. Our results show no significant preference of patients between ‘instant publication’ versus ‘publication after new information has been explained by a healthcare provider’. Overall respondents and experienced portal users had a strong preference to be able to communicate with their provider via a portal and to use a portal providing information from multiple providers. Lung patients preferred information from one provider and did not require the possibility to ask online questions.    Conclusions  Heart and vascular patients as well as lung patients prefer similar technical patient portal aspects, independent of their medical condition. Yet, in current portals consistency on this matter is lacking. It is highly assumable that offering a more consistent user-experience across the variety of patient portals could help increase patient portal acceptance, ultimately helping to stimulate patient engagement via patient portal use. We further affirm the need for customization on medical information publication and sharing information of various providers through patient portals, where information provision can be adapted to preferences of patients related to their medical condition(s).    Electronic supplementary material  The online version of this article (10.1186/s12911-018-0708-5) contains supplementary material, which is available to authorized users.

How do patients value and prioritize patient portal functionalities and usage factors? A conjoint analysis study with chronically ill patients