Fertility problems of mares on a well-managed breeding farm with thoroughbred stallions have been ascribed mostly to contamination of the reproductive apparatus of females with pathogens, particularly those of bacterial origin. This study presents a summary of the frequency of bacterial pathogens isolated from 437 cervical swabs which were collected from English thoroughbred mares intended for mating between 2008-2014, as well as of resistance tests of these pathogens to seven commonly used antibiotics as follows: penicillin, gentamicin, tetracycline, sulfisoxazole, cefotaxime, marbofloxacin and enrofloxacin. In addition, the study reports the changes in the levels of plasma oestradiol and progesterone determined two to three days before and two to three days after the first postpartum ovulation in mares with positive and dubious bacteriological findings and percentage of barren mares and mares that conceived at first, second and third post-partum ovulations. It was observed that 21.5% of mares were barren even after the third post-partum cycles. The oestradiol levels determined two to three days before the first post-partum ovulation were significantly lower in mares positive for pathogenic microflora in their reproductive apparatus compared to mares with the dubious findings (25.1 ± 5.8 pg/ml vs. 69.7 ± 18.3 pg/ml; P < 0.05), while the mean progesterone levels did not differ significantly but displayed a rather wide range in positive mares (from 0.08 to 1.38 ng/ml) compared to dubious mares with only small variations (0.12 ± 0.03 ng/ml). Moreover, of the total number of cervical swabs taken shortly before the first post-partum oestrus from all the mares intended for mating as many as 69.7% were contaminated with pathogenic microflora (positive findings). Saprophytic microorganisms only (the dubious findings) were isolated from 29.7% of swabs. From the 307 positive swabs, we could identify 40.4% positive for β-haemolytic streptococci and 20.4% positive for Escherichia coli, the pathogens implicated in causing reproductive disorders. Tests of antibiotic resistance of the investigated pathogens revealed that both Gram-positive and Gram-negative bacteria showed high susceptibility to antibiotics such as cefotaxime, marbofloxacin and enrofloxacin. On the other hand, both these bacterial groups showed high resistance to routinely used broad-spectrum antibiotics, such as penicillin and tetracycline. Because further research is required for a full understanding of the mechanism of pathogenesis of post-breeding endometritis, we can only hypothesise that uterine contamination with pathogenic microflora, particularly with β-haemolytic streptococci and coliform bacteria, diagnosed before the first post-partum ovulation, could negatively affect the hormonal regulation of oestrus and result in mare fertility problems.