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The objective of this study was to compare the accuracy of a uterine swab (US), a cytological brush (CB) and an endometrial biopsy (EB) to detect subclinical endometritis in mares. Cytological and bacteriological results of all three techniques were related to histological occurrence of polymorphonuclear neutrophils (PMNs) in the stratum compactum, commonly known as 'best standard'; to diagnose endometritis. Samples were taken from 55 mares of different breeds without clinical signs of endometritis. Samples for US, CB and EB were collected, smeared on a microscopic slide and cultured for bacterial growth. Endometrial biopsy samples were additionally stored in 4% formaldehyde for histological analysis. Bacteriological cultures and cytological samples of all techniques were classified as negative (no uterine pathogens in monoculture; < 2% PMNs) or positive (uterine pathogens in > 90% of the grown colonies; > 2% PMNs) for endometritis. Uterine pathogens were diagnosed in 20.0% of the mares. Isolation of pathogens was not associated with positive cytological findings (r = -0.23; P = 0.87). None of the six mares with an Escherichia coli infection (10.9%) showed a positive cytological result. In contrast, two of five mares infected with Streptococcus zooepidemicus had a positive cytological result. Histologically, the presence of PMNs in the stratum compactum was regarded as positive for endometritis when the mare was in diestrus at time of sampling. Compared to the 'best standard', sensitivity for cytology of CB, US and EB was 0.17, 0.00 and 0.25, respectively. Specificity for cytology of CB, US and EB was 0.83, 0.93 and 0.85, respectively. Sensitivity of uterine culture was 0.25, 0.33 and 0.25 for CB, US and EB, respectively. Specificity for culture of CB, US and EB was 0.80, 0.83 and 0.95, respectively. In conclusion, cytological or bacteriological examinations alone provide a high incidence of false negative results. Sensitivity of cytology combined with bacteriology of CB was 0.42. A combination of a bacteriological and a cytological examination of a CB sample improved the diagnostic performance in subfertile mares. Based on these results, we can recommend the CB to improve the diagnosis of subclinical endometritis in the mare compared to the US alone as currently used routine method.