Electrophoretic methods were used to identify protein complexes formed between ostrich egg yolk lipoprotein fractions (LPFo) with seminal plasma (SP) of fractionated ejaculates, and to investigate the effect of these complexes on boar semen quality after cryopreservation. Chromatographic SP fractions (F1, F2 and F3), with or without LPFo solution, were subjected to sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) analysis. Comparative electrophoretic analyses of the SP revealed marked differences in the SDS-PAGE protein profiles among boars. Electrophoretic analyses showed that the interactions of LPFo with SP resulted in the appearance of high-intensity protein bands. Spermatozoa were exposed to SP chromatographic fractions originating from F1, F2 and F3, and the whole SP (wSP) before being frozen. Spermatozoa exposed to F1 and F2 exhibited significantly higher post-thaw motility compared to those treated with either F3 or wSP. In most of the boars the proportions of membrane-intact frozen-thawed spermatozoa differed among the treatments, being significantly lower in the wSP-treated samples. The incidence of frozen-thawed spermatozoa with DNA fragmentation was less prevalent in samples exposed to F3 or the wSP. The results of this study confirmed that the interactions of LPFo with fractionated SP during the cooling period contributed to alterations in the sperm membranes, rendering them less susceptible to temperature-related injury.