This study was carried out to investigate the effect of uterine bacteriology and cytology on fertility in Thoroughbred horses during the period from April, 2008 to March, 2009 in Korea. About 91 strains were isolated from uterine culture swabs from 65 mares. The most common isolate was Escherichia coli (35 isolates, 38.5%) followed by Klebsiella pneumoniae (7 isolates, 7.7%), Streptococcus equi ssp. zooepidemicus (6 isolates, 6.6%) and organisms considered to be non-pathogens, other (43 isolates, 47.3%). Of the 65 cytological samples, 16 (24.6%) were positive for inflammation. The rate of pregnancy for normal, moderate and severe inflammation was 85.7, 42.9 and 22.2%, respectively. However, there are no significant relationship between bacteria and inflammation. In this study, researchers conclude that cytological examination of endometrium is a very effective method for a diagnosis of endometrial status. This research will contribute to the horse breeding industry including production of riding horses by artificial insemination as well as racing horses in Korea.