Equine hygiene: good practices for breeding activities


Strict hygiene measures must be taken during breeding activities in order to prevent pathogens from being spread between breeding animals. To be effective, these measures must be applied across the stud farm as well as to the individual animals.


Breeding hygiene measures have the following objectives:

  • prevent the stallions and mares from being contaminated by pathogens, i.e. germs capable of developing in the mare’s uterus and causing extended inflammation or endometritis,
  • reduce the quantity of microbes typically found on the genital mucous membranes. The genital mucous membranes provide an ideal environment for microbes to develop by offering warmth, moisture and nutrient-rich secretions. This bacterial flora varies. In exceptional cases it can become dangerous for the uterus.

General stud farm hygiene

During covering, germs are passed between the breeding animals © L. Marnay

The objective of stud farm hygiene rules is to prevent the transmission of pathogens (= which cause disease) between breeding animals.

Pathogens are passed between breeding animals:

  • during covering (during contact between the genital mucous membranes of a contaminated stallion and a healthy mare or, vice versa, a contaminated mare and a healthy stallion),
  • during artificial insemination (only when the semen of a contaminated stallion is passed on to a healthy mare),
  • indirectly via media coming into regular contact with the genital organs.

Any media (material or manual) that come into contact with the genital organs must be sterilized or, failing that, single-use or reserved for an individual animal.

In practice:

  • the handler must wear single-use gloves to take control samples on the stallion’s penis, guide the penis into the vagina, bring the mare to the stocks and wash her vulva, and wear sterile gloves or, failing that, single-use glovesto inseminate a mare or take samples from the cervix or clitoris.
  • equipment that comes into contact with the genital organs must be single-use (paper towel, tail guard, artificial vagina inner liner, plastic bag at the back of the breeding mount, which must be changed after each collection, insemination catheter and glove, vaginoscopes, etc.) or sterile.

Hygiene for the mare

Use sterile equipment or, failing that, single-use equipment

Hygiene rules for the mare aim to reduce the quantity of germs that could potentially enter the uterus.

A very large quantity of germs are found on the mare’s vulva. Moving up the genital tract this quantity decreases gradually, and the uterus is free of germs (sterile).

This gradual decrease in the microbial population is explained partly by the difficulty with which germs enter the genitalia (due to the three barriers formed by the vulva, the vestibular seal and the cervix) and partly by the immune defenses of the uterus, which eliminate them.

The usually sterile uterus receives germs during procedures such as covering or insemination (in the semen, during gynecological operations in the vagina or due to an abnormal vulval conformation (allowing air into the uterus carrying a few germs in suspension)) and during foaling. It reacts with an inflammatory response that eliminates the germs (within 1 or 2 days following covering, for example).

The ability of the uterus to fight germs varies from one mare to another and throughout the cycle (it is high during the estrous phase and very low outside this phase).

The uterus must be protected from germs. Otherwise its immune defenses are likely to be overcome, resulting in endometritis.

In practice:

  • only insert sterile equipment (glove, insemination catheter, embryo recovery probe, uterine swab, etc.) into the vagina, cervix or uterus of a mare,
  • thoroughly clean the perineal area, which is highly soiled, before inserting anything in the vagina (wash 3 times with an iodine antiseptic soap, rinse each time with warm water, wipe).

Hygiene for the stallion

Soaking the penis after collection, in a pot allocated to the stallion © Ifce

Hygiene rules for the stallion aim to keep the penis clean while maintaining the biological balance of its bacterial flora.

The mucous membrane of the penis is covered in an extremely rich microbial flora. These are the germs found in semen during covering or semen collection. This microbial flora protects the penis against other more dangerous germs. It is important to maintain the biological balance of this flora.

Antiseptics must never be used on a stallion’s penis as this could result in colonization by harmful bacteria. They must only be used exceptionally to treat a pathogen on a carrier stallion as prescribed by a veterinary surgeon. Rinsing the penis with warm water is usually all that is required.

In practice:

  • after sexual rest or when the penis looks dirty, wash it with warm soapy water, rinse and wipe dry.
  • after each covering, dip the penis in a pot of clean water.
  • before each collection, rinse the penis in clean water in order to remove most of the dirt, and wipe dry.

Hygiene during artificial insemination

Hygiene rules during artificial insemination aim to prevent the semen being contaminated with additional germs during the successive semen handling operations.

Insemination has significant health advantages over natural covering. It:

  • eliminates the transmission of pathogens from mare to stallion.
  • reduces the number of germs deposited in the uterus (500,000 germs/ml in ejaculated semen, compared with 3,000 to 13,000 germs/ml in insemination doses).

In practice:

  • all equipment in contact with semen must be sterile (collection bottle, catheter, syringe, filtration cone and mesh, etc.).
  • only inseminate mares when they are in heat.
  • thoroughly clean, rinse and dry the vulvar area before inseminating the mare, and use sterile catheters protected with suitable sheaths.

The latex cones used for semen collection must be soaked, cleaned, rinsed in clean water followed by demineralized water, dried and stored in a dust-free place, thus eliminating one source of contamination. 

© Ifce