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Semen jets in the stallion’s ejaculate differ in both the biochemical composition of seminal plasma (SP) and in sperm concentration, forming sperm-rich fractions (HIGH) and sperm-poor fractions (LOW). This study examined (i) the association of the levels of selected components of SP [alkaline phosphatase (AP), acid phosphatase (ACP), Na+, Cl-, K+, Ca, Mg and prostaglandin E2] with semen quality, sperm longevity and fertility; (ii) the effects of the presence of SP on sperm survival during cooled storage; (iii) the differences in the composition of SP between sperm-rich and sperm-poor ejaculatory fractions; (iv) the differences between these fractions in the effects of SP on sperm longevity. The levels of AP, ACP and Na+ were higher in HIGH compared with LOW, whereas higher concentrations of Ca, K+ and Mg were found in LOW than in HIGH. None of the measured components were correlated to the first cycle pregnancy rate. The presence of SP during cooled storage caused DNA degradation, but total and progressive sperm motility was not affected. Sperm-rich fractions stored with low levels of SP maintained higher level of DNA integrity compared with sperm-rich fractions in higher levels of SP, or sperm-poor fractions irrespective of the proportion of SP. The concentration of K+ in LOW may give some indication on the maintenance of total sperm motility during cooled storage.