Changes in the concentrations of individual flavonoids and polyamines (PAs) in Scots pine (Pinus sylvestris L.) cotyledonary seedlings were studied during the establishment of an ectomycorrhizal (ECM) symbiosis with two Suillus variegatus strains in vitro. Both flavonoids and PAs were analysed after 3, 7, and 14 d in dual culture, and changes in concentrations were compared with growth of the seedlings. Both S. variegatus strains caused similar responses in Scots pine seedlings. Free putrescine accumulated immediately but only transiently after inoculation. This was followed by continuous accumulation of PA conjugates in needles and stems, and free spermidine and spermine in roots, which was accompanied by mycorrhiza formation and improved growth. The fungi induced lateral root formation and main root and primary needle elongation. Inoculation caused no qualitative changes in flavonoid composition, while quantitative changes in flavonols, catechins, and condensed tannins were observed in shoots during mycorrhiza formation. These results indicate that in this in vitro system conjugated PAs and specific flavonoids, generally related to the plant's defence reactions, did not play a major role in the regulation of the establishment of the ectomycorrhizal (ECM) symbiosis in Scots pine roots. The results also clearly show that positive growth responses in shoots and roots due to S. variegatus were supported by different and highly specific changes in the synthesis of both primary and secondary metabolites in these parts of the seedling.