Background There is little research on laypersons’ perceptions regarding common cold and influenza, their symptomatic distinction and considerations of risk. This study investigates understanding of pathogenesis across three European countries and provides a knowledge base from which adequate prevention recommendations and treatment advice can be derived. Methods This is a qualitative research study. Semi-structured face-to-face interviews were conducted with 85 participants from three European countries (Austria n = 31, Belgium n = 30, Croatia n = 24) about their experiences, perceptions and risk considerations regarding the common cold and influenza. We performed a qualitative thematic content analysis. Results Three main themes were identified: common cold as harmless with individualistic symptoms; influenza as mainly distinguishable by fever, confinement to bed and severity of symptoms, but description about onset and duration are diverse; and views on pathogenesis contain references to disease causing agents and circumstances. Overall we found that risk perception is based largely on personal experience and risk is assumed moderate for both diseases. Conclusions Study participants possessed a fairly good understanding of symptoms, differences and pathogenesis of common cold and influenza; but explanations integrated misconceptions, such as misinterpretation of fever, disease continuums, diverse onset ideas etc. Perceptions were largely based on lived experiences and interventions for prevention and treatment should be led by health care workers and focus on these issues. Basic consultations, awareness raising activities and other knowledge disseminations strategies should include aspects of communicableness and the self-limiting nature of both diseases. An informed understanding of both infectious diseases is crucial and may also increase influenza vaccination coverage in the three respective countries effectively.