Furan fatty acids (F-acids) are a class of natural antioxidants with a furan moiety in the acyl chain. These minor fatty acids have been reported to occur with high proportions in the cholesteryl ester fraction of fish livers. Here we present a method for the direct analysis of intact cholesteryl esters with F-acids and other fatty acids in cod liver lipids. For this purpose, the cholesteryl ester fraction was isolated by solid phase extraction (SPE) and subsequently analyzed by gas chromatography with mass spectrometry (GC/MS) using a cool-on-column inlet. Pentadecanoic acid esterified with cholesterol was used as an internal standard. GC/MS spectra of F-acid cholesteryl esters featured the molecular ion along with characteristic fragment ions for both the cholesterol and the F-acid moiety. All investigated cod liver samples (n = 8) showed cholesteryl esters of F-acids and, to a lower degree, of conventional fatty acids. By means of GC/MS-SIM up to ten F-acid cholesteryl esters could be determined in the samples. The concentrations of cholesteryl esters with conventional fatty acids amounted to 78-140 mg/100 g lipids (mean 97 mg/100 g lipids), while F-acid cholesteryl esters were present at 47-270 mg/100 g lipids (mean 130 mg/100 g lipids).