Compound-specific isotope analysis (CSIA) of fatty acids is a relatively young analytical method. However, CSIA of fatty acids has increasingly become the method of choice in areas where accurate and precise knowledge of isotopic composition at natural abundance level is important. CSIA of fatty acids at natural abundance level provides information on biogenetic and geographic origin of lipids and oils that is invaluable for research into archaeology and the environment and almost indispensable these days for authenticity control and fraud detection in food analysis. In combination with naturally enriched or stable isotope labelled precursors, CSIA of fatty acids has also gained increasing importance in biochemical, -medical and -geochemical applications as it offers a reliable and risk-free alternative to the use of radioactive tracers.