Compound-specific carbon and hydrogen isotopic compositions of lipid biomolecules (n-alkanes, n-alkanoic acids, n-alkanols, sesquiterpenes, diterpenes, phytol, diterpenols and beta-sitosterol), extracted from Cryptomeria japonica leaves, were determined in order to understand isotopic fractionations occurring during lipid biosynthesis in this species. All lipid biomolecules were depleted in both 13C and D relative to bulk tissue and ambient water, respectively. n-Alkyl lipids associated with the acetogenic pathway were depleted in 13C relative to bulk tissue by 2.4-9.9 per thousand and depleted in D relative to ambient water by 91-152 per thousand. C(15)- and C(30)-isoprenoid lipids (sesquiterpenes, squalene and beta-sitosterol) associated with the mevalonic-acid pathway are depleted in 13C relative to bulk tissue by 1.7-3.1 per thousand and depleted in D relative to ambient water by 212-238 per thousand. C(20)-isoprenoid lipids (phytol and diterpenoids) associated with the non-mevalonic-acid pathway were depleted in 13C relative to bulk tissue by 4.6-5.9 per thousand and depleted in D relative to ambient water by 238-303 per thousand. Phytol was significantly depleted in D by amounts up to 65 per thousand relative to other C(20) isoprenoid lipids. The acetogenic, mevalonic-acid and non-mevalonic-acid pathways were clearly discriminated using a cross-plot between the carbon and hydrogen isotopic fractionations.