Mice in hay

When mice levels are high, producers should be mindful that stored hay, or the hay you are buying in, could have some level of contamination from mice.

What's the risk of mice contaminated hay?

Mice not only do damage, they carry disease that can pose a risk to livestock.

It is important producers consider their options before using or purchasing potentially contaminated hay, as it can carry risks, such as:

  • Livestock avoiding hay due to smell
  • Leptospirosis in cattle
  • Botulism in livestock.

A major risk is that mice urine can spread Leptospirosis, commonly known as “Lepto”.  There are more than 250 different serovars (or “strains”) of Lepto. Two of these strains (L.hardjo and L.pomona) are known to cause abortion in cattle, and there is a vaccine available to prevent this. Hence, I would strongly recommend if you are planning on feeding out hay that has been contaminated by mice, that you fully vaccinate your cattle for Lepto well in advance of feeding (this means giving them two shots, 4-6 weeks apart). There is no vaccine available for sheep, but Lepto is not thought to cause clinical disease in sheep.

Mice carry many more strains of Lepto than just two though, and these other strains may infect humans that are handling the hay. Lepto is a debilitating zoonotic disease and there is no vaccine for people, therefore the best way to reduce the risk is to limit contact with mice urine. You may choose to do this by electing not to use the hay, using mechanical methods to move the hay so that people aren’t handling it, or wear appropriate PPE (long clothing, gloves, eye protection and a mask) when touching the hay.

Another real risk that can come from mice contamination of hay is Botulism. Botulism comes from a bacterial toxin that lives in the dead mice carcasses. When livestock eat the hay and pieces of the carcasses, they may become infected.  It causes flaccid paralysis which results in animals that go down, cannot eat and drink and eventually die. Large numbers of stock may be affected and there is no treatment. Vaccination is available for cattle and sheep for botulism, but two shots are needed for most products available on the market, so again, plan ahead.

It may be prudent to vaccinate for botulism, regardless of whether you are planning to feed hay, due to the extreme contamination of paddocks with mice carcasses. Stock that are phosphorus or protein deficient will actively select to chew on carcasses and bones and are at a higher risk.

Assessing damage to hay bales

Monitoring is key when identifying the impact of mice on hay bales. Where possible, open them up and examine from various positions or sections of the haystack or shed. An assessment of the damage can be made by identifying the number and depth of mice holes and the amount of carcasses, urine of feces found.

For low levels of damage, it may be possible to remove damaged sections, and destroy them separately. However, this would only reduce your risk, not fully remove the possibility of the fodder source continuing to be contaminated.

When inspecting bales, it is important to wear personal protective equipment (PPE) and implement good hygiene practices. Mice damaged also pose a hazard because they can collapse.

What to do with mice damaged hay

Mice contaminated hay can be managed through burning, burying or spreading. When deciding which option is most appropriate, you should consider the quantity needing to be disposed, cost and local weather conditions.


Burning contaminated hay bales, in an isolated and open area, can be a cost-effective means of disposal. This practice requires minimal input but can be quite time-consuming if dealing with large quantities of hay and conditions are not conducive.

If employing this practice, be sure to comply with all NSW Rural Fire Service (RFS) requirements and implement appropriate strategies to mitigate the risk, such as firebreaks and access to water carts.


Burying contaminated hay in carefully chosen sites can be a suitable option for large amounts of hay, but cost and availability of machinery should be considered.

Pit locations should avoid sites prone to accumulating water or near water ways. Pits need to be deep enough to apply a minimum of a foot of soil between the additive height of the bales and the original soil surface. Excess soil must then be placed on top to compensate for future sinking of the pit.

Unlike other pits, these will not require lining, but will still require livestock to be restricted access from the site.


Hay may be spread back onto paddocks. Spreading contaminated hay across a paddock with rakes can put nutrients, bound in the organic matter, back into the soil through decomposition. This will take a significant time to occur but may provide some benefit out of hay that can carry risks to livestock.

If you’ve been poisoning mice using either anti-coagulants or zinc phosphide, the actual bait itself is a poisoning risk to livestock if present in the hay when it’s fed out, however secondary poisonings of livestock from eating the carcasses is low.

More information

For more tips and advice, you can read ‘What to do with mice damaged hay ’ by Tim Bartimote, Local Land Services Cropping Adviser.

For more information on managing mice impacted hay, contact your local vet or agricultural advisor.

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