Background: The breeding prognosis for a mare with fungal (yeast or mold) endometritis is generally considered poor. To our knowledge, however, no reports have been published on the expected pregnancy rate for mares diagnosed with a fungal infection. Study design: Insemination records from 3,223 mares inseminated at two stud farms were retrospectively examined. Mares diagnosed with fungal endometritis were all treated with uterine lavage using physiological saline, intrauterine deposition of 100 mg Clotrimazole vagitorial tablets and oxytocin (10 i.e., i.m.) for three consecutive days. Methods: From mares with signs of endometritis microbiological culture and cytological assessment were performed on endometrial biopsies. The per season pregnancy results were compared between affected and unaffected mares. Results: A total of 686 mares out of 3,223 mares were considered to have endometritis. Based on the endometrial biopsies obtained, 377 (55%) had no growth, 50 (7.2%) had growth of yeast, 2 (0.3%) had growth of mold and 257 (37.4%) had growth of bacteria recorded. Positive cytology was found in 78.0% of samples diagnosed with yeast endometritis whereas that was the case in 65.6% of samples showing growth of mold or bacteria (P = 0.12). The per-season pregnancy rate was 48% in mares diagnosed with yeast endometritis. The overall per season pregnancy rate in the two stud farms was 76.4% (P < 0.0001, Odds ratio = 3.59, confidence interval 95% = 2.04–6.29). Conclusions: Yeast can make up a considerable cause of endometritis. The breeding prognosis of a mare with yeast endometritis must be considered worse than that of a normal mare. Following management of the condition approximately 50% of the mares previously diagnosed with an endometrial yeast infection got in foal rendering the breeding prognosis better than initially anticipated.