PurposeFunctional foods have been marketed as promoting health and reducing the risk of disease. While the market of functional foods is increasing across the globe, little is known about how actual and subjective health status are related to functional food choices and existing research evidence is inconsistent. Therefore, the purpose of this paper is to systematically explore the relationship between functional food choices and perception related dimensions vs medical dimensions.Design/methodology/approachThe study used data collected from a large-scale mail survey in Japan (N = 8,368) and a representative Internet survey in Lithuania (N = 900). It used structural equation modeling (SEM) to test the proposed conceptual model.FindingsThe general results indicated that functional foods could be used to maintain one’s subjective health status – the frequency of using functional food products was positively related to consumers’ subjective health status (p = 0.04). However, if consumers were experiencing health-related issues (self-reported disease symptoms or current medical treatment), there was no systematic relationship between such experience and the usage of functional food products.Originality/valueTo the best of the authors’ knowledge, this study is among the first to systematically analyze the relationship between subjective health status, self-reported disease symptoms, current medical treatment and the frequency of using different functional food product groups. The findings indicated that it is important to simultaneously consider different underlying factors, such as specific to functional food targeted disease symptoms and specific food product groups, which contributed to a more thorough understanding of functional food consumption.