Endometritis in the mare begins as a normal physiological inflammatory response to breeding that involves both a mechanical and immunological response pathway activated to rid the uterus of semen and bacteria. With successful resolution of this inflammation, the mare‘s uterus will provide a hospitable environment for the development of the semi-allogenic conceptus. If the mare fails to resolve this inflammatory response within 48 h of breeding, she will become susceptible to persistent breeding-induced endometritis (PBIE) which will have detrimental effects on her fertility. This condition can then predispose the mare to bacterial or fungal endometritis leading to further degeneration of the endometrium. Optimisation of the mare’s fertility requires a fine balance between allowing the natural immune response of the endometrium to its exposure to allogenic semen to run its course, and yet preventing its progression to PBIE or the involvement of infectious agents. This review discusses the challenges presented by PBIE, latent infections, biofilms, fungal infections and the need to utilise diagnostic methods available and implement targeted treatments to optimise fertility in the mare.