Artificial insemination using cooled, transported semen has become a popular practice in the equine industry. However, equine sperm are assumed to show a decline in their fertilizing ability after 24 to 48 hours of cooled storage. Two measures that are commonly used to estimate the fertility of an ejaculate are sperm motility and sperm membrane integrity (SMI). Recently, it has been suggested that SMI may have a better correlation with fertility of an inseminate than sperm motility. The effect of cooled-storage on sperm quality over an extended time period was evaluated to illustrate changes in sperm characteristics that might be related to an ejaculate’s fertility. Semen was stored at 4°C in INRA 96 extender containing 10% seminal plasma for a period of 10 days. Data were collected daily on sperm motion characteristics, SMI, mitochondrial membrane potential, and DNA quality. To measure daily changes in SMI in stallion sperm, two fluorescent vital-staining protocols used in flow cytometric analysis were compared – a combination of SNARF-1, Yo-Pro-1, and Ethidium Homodimer 1 (SYE) and a combination of lectin from Pisum sativum and propidium iodide (PSA/PI). We hypothesized that the SYE protocol adapted for use with stallion sperm could detect more subtle, and perhaps earlier, damage to the sperm plasma membrane than the PSA/PI protocol. A combination of SYBR 14, propidium iodide, and JC-1 (SYPIJC) was used to measure mitochondrial membrane potential, as well as SMI. A computer-assisted sperm motion analysis (CASA) instrument was used to evaluate sperm motion characteristics; the sperm chromatin structure assay (SCSA) was used to measure the degree of DNA fragmentation. In this study, with the exception of sperm motility, the measures of sperm quality retained values consistent with “viability” after 10 days of cooled-storage. This suggests that the fertility of some stallions may last considerably longer than previously assumed, which could ultimately alter the time-table used for artificial insemination using cooled, transported semen.