The objective of the present study was to examine differences in the fatty acid composition of subcellular fractions from normal and cancerous parts of human testes. The conjugated linoleic acid (CLA) content was significantly higher in total testicular carcinoma (TC), but significantly lower in the mitochondrial fraction of TC in comparison to normal testicular tissue. The subcellular distribution pattern of CLA was similar to that of monounsaturated fatty acids, but different to that of 18:2n-6 (linoleic acid), underlining the different physiological properties of CLA and 18 : 2n-6. Because polyunsaturated fatty acids (PUFAs) have been suggested to have an effect on cancer risk and previous research has found that CLA inhibits the metabolism of 18 : 2n-6 into 20 : 4n-6, the contents of n-6 and n-3 PUFAs were determined. Significant differences were observed for 18 : 2n-6, 18 : 3n-3, 20 : 5n-3, and 22 : 6n-3, with 18 : 2n-6, 18 : 3n-3, and 20 : 5n-3 contents being higher and 22 : 6n-3 content being lower in TC than in normal testicular tissue. These results indicate a changed availability of substrates for the cyclooxygenase (COX) or lipooxygenase (LOX) pathways generating eicosanoids. Although not statistically significant, the reduced content of 20 : 4n-6 shown in this study might be due to an increased metabolism of this fatty acid into eicosanoids.