Carbohydrates and lipophilic compounds constitute an important component of litter and soil organic matter in boreal forests, but are still poorly identified. We characterized needle litter and coarse tree litter (cones, seeds, bark and twigs) from coniferous trees (Pinus sylvestris L. and Picea abies Karst.), and moss litter (Pleurozium schreberi, Hylocomnium speldens), fermentation (F) and humus (H) layers in four boreal forest sites in Finland using a combination of sequential fractionation (non-polar extractions, NPE; water-soluble extractions, WSE; acid-soluble fraction, AS) and detailed analyses on the soluble fractions using GC-MS. Comparisons among the different layers of the soil organic horizon were used to assess which lipophilic compounds and carbohydrates increased in the F and H layers in proportion to their relative abundance in the litter layer and thus might have a large potential to accumulate in soil organic matter. Both concentrations and relative proportions of different compounds varied among the soil layers. Several of the fatty acids (FAs) found in the litter samples were absent in the F and the H layers. Needle and coarse tree litter contained a wide range of di- and triterpenes, but in the F and H layers oxidized forms of dehydroabietic acid and sterols were abundant. The large proportion of dehydroabietic acid in the lipophilic fraction in the H layer suggests that it may be poorly degradable by soil microorganisms, probably because of its anti-microbial function in trees. The composition of the acid-soluble fraction indicated that the proportion of cellulose in relation to hemicelluloses increased from the litter layer to the F and H layers. Put together, changes in the relative proportions of organic compounds in soluble fractions indicate that selective preservation of compounds, litter input by plant roots and microbial synthesis of compounds all contribute to the accumulation of aliphatic compounds in the H layer of boreal forests.