We describe a simple and sensitive method to identify and quantitate long-chain fatty alcohols. Long-chain fatty alcohols were converted to their pentafluorobenzoyl derivative and analyzed by gas chromatography (GC)-mass spectrometry in the negative ion chemical ionization (NICI) mode with selected ion monitoring. GC resolution was obtained for myristyl, palmityl, heptadecyl, stearyl, oleyl, linoleyl and arachidonyl alcohols. As little as 0.4 fmol of fatty alcohol can be detected, which represents a six order-of-magnitude increase in sensitivity over previously described methods. This assay can be used to measure femtomolar amounts of long-chain acyl coenzyme A thioesters after reduction to the corresponding fatty alcohols with sodium borohydride. Other potential applications of this assay include identification and quantitation of long-chain fatty alcohol production by microorganisms.