The cold storage and cryopreservation of semen decrease sperm quality. Morphological and biochemical analyses of spermatozoa provide valuable information for the optimization of storage protocols to obtain a sufficient number of spermatozoa for in vitro fertilization. The aim of this study was to evaluate the morphology and lipid composition of Atlantic salmon (Salmo solar) spermatozoa after storage at 4 degrees C and cryopreservation. Semen samples were obtained by stripping. One aliquot was stored at 4 degrees C for 7 days, and another aliquot was cryopreserved. The morphology and ultrastructure were analysed using electron microscopy. The lipid composition was analysed by gas chromatography and a commercial kit. After cold storage, the mitochondrion was the most affected component; however, plasma membrane rupture and detachment of the flagellum were also observed. Morphological abnormalities were greater in cryopreserved spermatozoa. The head and mid-piece were dehydrated, sperm membranes were vesiculated, and alterations of mitochondria were observed. After cold storage and cryopreservation, there were less polyunsaturated and omega-3 fatty acids. Furthermore, there was an increase in saturated fatty acids and decrease in cholesterol concentration after cryopreservation (P < 0.05). Based on the results, cryopreservation drastically damaged sperm membranes; the cryogenic damage was associated with membrane lipid composition alterations. The sperm membranes were affected less by cold storage but there was also a decrease of some lipids; therefore, there is a need for improvement in cold storage processes to decrease structural damage of spermatozoa so that semen cryopreservation can be effectively used in the salmon industry.