A great deal of attention has recently been given to the essential role of polyunsaturated fatty acids (PUFA) of sperm membranes. We studied the fatty acid composition of the immature germ cells (IGC) and of the sperm populations separated by Percoll gradient in the ejaculate of normozoospermic patients. Fatty acid pattern was analysed by combined gas chromatography–mass spectrometry on a capillary column. In IGC, differences were found compared with mature spermatozoa, with a higher percentage of saturated fatty acids and of essential fatty acids. On the contrary, the long-chain PUFA were significantly lower in IGC. The highest concentration of n3 PUFA docohexaenoic acid (DHA) was detected in the spermatozoa deriving from 70–100% Percoll layers and a direct linear correlation was found between the increase of DHA and increased percentage of Percoll gradient. An inverse relationship between the percentage of atypical sperm forms in each layer and the percentage of DHA was also observed. This study demonstrates that the human germ cell line can elongate and desaturate essential fatty acids and that the percentage of long-chain PUFA is correlated with the normal morphology of sperm cells.