Medicinal plants and their products are popular in Estonia. There are two approaches to use of herbal products: first, that based on traditions and practical experience and, second, that supported by scientific evidence. It is important to marry these two approaches. One place where traditions and new knowledge could meet is the pharmacy. In this study we evaluated knowledge about the use and safety of herbal products of pharmacy customers in South-Estonia. A convenience sample of pharmacy customers in south Estonia (n = 196) participated in the study. Of the survey participants, 76% were frequent or occasional users of herbal products and considered these products safe (75%) and effective (73%). Herbal products were mostly (91%) consumed for prophylaxis or treatment of minor illnesses. Main information sources about herbal products were pharmacists (75%) and package information leaflets (65%). Mode of action (95%), administration (81%) and indication (77%) were the information details more frequently sought from the pharmacy about herbal products. Of the survey participants, 22% described some problems connected with the use of herbal products. Herbal products are popular in Estonia and pharmacists have an important role in counselling on these products. Despite knowledgeable use of herbal products and infrequent experience of side effects with these products, safety issues should be more stressed in the providing of information details to pharmacy customers.