The annual variation and anatomical distribution of fatty acids in the burrowing bivalve, Mya truncata, were studied at five different times between May 1997 and July 1998, in Isfjorden, Spitsbergen. Twenty-eight fatty acids were determined by direct methanolysis of samples from various tissues, gas chromatography and statistical, principal component analysis of the chromatographic results. Gill, foot and mantle tissue, as well as gonads and stomach contents, were subjected to analysis. The branched fatty acid, 4,8,12-trimethyltridecanoic acid occurred in about 3% relative abundance in the stomach contents in all animals, originating from ingested phytoplankton. This acid was either not assimilated but excreted directly or, if assimilated, it was completely catabolised. The fatty-acid composition of the stomach contents varied significantly with time of sampling, indicating variation in the phytoplankton community in the bottom water. The gill, foot, mantle and gonad tissue had mutually different fatty-acid composition, all significantly different from the composition of the stomach contents. This shows that the tissues have typical fatty-acid composition, and that assimilated fatty acids are subject to modification and/or selection before being incorporated into tissue lipids. This was further substantiated in that the rather large temporal changes in fatty-acid composition of the stomach contents were not mirrored in the tissues. However, a minor effect of the changes in the diet was detected in the gill tissue. Male and female gonads had significantly different fatty-acid compositions, with C20 and C22 acids more abundant in the male gonads and C16 and C18 acids more abundant in the female gonads. Fatty-acid analysis may be used in identification of the sex of the bivalves.