Scots pine (Pinus sylvestris L.) is known as an economically important forest tree with a wide distribution throughout the Northern hemisphere. Recently, the species has also become recognized as a novel source of functional food and bioactive compounds with medicinal properties. The present paper provides up-to-date information on protocols for somatic embryogenesis (i.e., the most promising in vitro method for vegetative propagation of Scots pine). Endophyte protocols cover the topics of endophyte isolation, identification and elimination from in vitro cultures. Moreover, the protocols for secondary metabolite analyses are described in order to emphasize the emerging role of Scots pine as a medicinal plant.