Central and Eastern European countries Romania and Moldova are rich in botanical and medicinal traditions. However, limited information is available about ethnobiological studies including use of medicinal plants in self-medication of minor illnesses. The aim of this study was to collect contemporary evidence about treatment options of the common cold and influenza with medicinal plants among pharmacy customers of two neighbouring countries: Romania and Republic of Moldova, including the self-proclaimed region Transnistria. A cross-sectional survey was undertaken in community pharmacies of Romania, Moldova and Transnistria in 2017. The pharmacy customers enrolled in the study completed a survey instrument evaluating perceived characteristics and action taken in case of common cold or influenza symptoms. A considerable proportion of the respondents used self-treatment options based on OTC medicines and/or medicinal plants. Survey respondents used professional (general practitioner, pharmacist) and non-professional (family and friends) information sources to learn more about medicinal plants. Medicinal plants were frequently used and considered effective in the treatment of the common cold and influenza. However, there are different use patterns of medicinal plants against the common cold and influenza among patients in Romania and Moldova. More common medicinal plants used in all three regions were lemon, raspberry and garlic, which were considered effective in monotherapy or in combination with non-prescription medicines.