Despite a long history of the use of Pinus thunbergii for technical, medicinal, agricultural, and other purposes, the composition of low-volatile metabolites in the used parts of the plant has been poorly investigated. We report here on the distribution of lipophilic extractive compounds in different parts of the shoot system (needles, defoliated twigs, outer bark) of P. thunbergii studied by GC/MS. The highest and lowest contents of lipophilic substances were found in defoliated twigs and in outer bark correspondingly. Acid compounds in the extract of needles comprised mainly labdane type diterpenoids (trans-communic acid), while in the extracts of defoliated twigs and outer bark the acids were represented predominantly by abietane type compounds (neoabietic, dehydroabietic, abietic, levopimaric and palustric acids). The major neutral components of the extract of needles were 10-nonacosanol, labdanoids (18-hydroxy-1 3-epi-manoyl oxide, trans-communol), and beta-sitosterol. In the case of the extract of defoliated twigs, labdanoids (18-hydroxy-13-epi-manoyl oxide, trans-communol, 13-epi-torulosol), serratane triterpenoids (3beta-methoxyserrat-14-en-21-one), and beta-sitosterol were the main neutral constituents, whereas serratanoids (3beta-methoxyserrat-14-en-21-one) alone dominated among the neutral compounds of the outer bark extract. Most of the neutral components and the labdane type acids were detected for the first time in organs and tissues of P. thunbergii. The distribution of lipophilic metabolites in the studied parts of P. thunbergii shoot system may be applied for chemotaxonomy purposes. Diversified accumulation of extractive substances in different organs of the plant should be taken into account for isolation of specific components from the pine raw material.