Purpose This study was performed to investigate whether removal of cholesterol from the plasma membrane and collapse of the acrosome can prevent structural chromosome aberrations of paternal origin in mouse zygotes produced by intracytoplasmic sperm injection (ICSI). Methods Mouse spermatozoa were treated with methyl-β-cyclodextrin (MβCD) to remove cholesterol from the plasma membrane and with calcium ionophore A23187 to collapse the acrosome. Chromosomes of zygotes derived from MβCD-and ionophore-treated spermatozoa were analyzed at the first mitotic metaphase. Results Both chemical agents effectively induced the acrosome reaction. Incidence of structural chromosome aberrations in ICSI zygotes derived from MβCD-treated spermatozoa was similar to that in zygotes produced by in vitro fertilization (IVF) with the same spermatozoa, but significantly lower compared to ICSI zygotes derived from acrosome-intact spermatozoa. Chromosome aberration rates in ICSI zygotes derived from ionophore-treated spermatozoa were evidently high compared to IVF zygotes. Conclusions Induction of the acrosome reaction through cholesterol efflux by MβCD can prevent chromosome aberrations of paternal origin, while use of ionophore to induce the acrosome reaction exerts detrimental effect on paternal chromosomes in ICSI zygotes.