Fly strike in rabbits and guinea pigs - what to look out for

Flies are annoying for people, particularly in the summer months. But for our rabbits and guinea pigs some flies present a potentially fatal threat, as they can cause fly strike. While it can be dangerous and life-threatening, fly strike is very easy to prevent if you know how. If your rabbit or guinea pig has fly strike, go directly to the section on 'what to do if my pet has fly strike'.

What is fly strike?

Fly strike occurs when blow flies, or green bottles, lay their eggs on an animal, usually around the bottom area. These eggs then hatch into maggots which eat the animal’s flesh. As the maggots feed, the dying tissue releases harmful toxins into the animal’s bloodstream. In severe cases this can cause septicaemia (blood poisoning) and death. Fly strike mostly affects rabbits or guinea pigs, but it can occur in any animal.

How do rabbits and guinea pigs get fly strike?

Rabbit Fly StrikeThe biggest cause of fly strike in rabbits and guinea pigs is poor hygiene, either of the pet itself or the environment. Urine, faeces and open wounds all attract flies. While many small animals are good at keeping themselves clean, sometimes other factors can put them at risk.

Causes and risk factors of fly strike include:

  • An overcrowded hutch
  • Dirty bedding or toilet area
  • Your pet being unwell with diarrhoea
  • Your pet being unable to move or clean themselves properly due to dental problems, old age, illness or obesity
  • Ungroomed, long-haired rabbits and guinea pigs may get urine or faeces matted around their bottoms
  • Open wounds


Fly strike is particularly a problem in the summer. But if the environmental conditions for flies are correct, it can occur at any time. Contrary to popular belief, indoor pets are also at risk and we should take suitable precautions.

As well as causing fly strike, flies can infect rabbits with myxomatosis. This disease can be fatal, but fortunately can be often be prevented through regular vaccinations. This is another reason to ensure you keep your pets' house clean and prevent the attraction of flies.

Guinea pig in the grassWhat are the signs and symptoms of fly strike in rabbits and guinea pigs?

The most obvious sign of fly strike is an infestation of maggots, usually around your pet's bottom. If fly strike is only detected at this stage you need to act quickly, as detailed in the next section. Other signs of fly strike to look out for are the risk factors mentioned above, such as diarrhoea or illness, and of course, an increased amount of flies around your pets' home.

Check your pets' bottoms once a day, twice a day in the summer for signs of fly strike. Also keep an eye on your pets' faeces, weight and dental health. You should check your rabbits or guinea pigs for signs and symtoms of illness every day. Loss of appetite, changes in eating, drinking or toilet habits can all be signs that something isn't right. This could be due to fly strike or something else.

What do I do if my rabbit or guinea pig has fly strike?

If your rabbit or guinea pig has fly strike, it is important to act straightaway. Seek veterinary attention IMMEDIATELY for rabbits and guinea pigs infested with maggots. Any delay could cause the death of your beloved pet.

If you have caught fly strike early enough, you may be able to treat your rabbit or guinea pig at home by following the steps below. If you cannot take your pet to the vet straightaway, follow these steps as an interim treatment.

  • Keep your rabbit or guinea pig warm. Carefully clip off or remove any matted fur and faecal material.
  • Fill a suitable container with clean, warm water. If you have an appropriate pet shampoo, such as Beaphar Guinea Pig and Rabbit Shampoo, add this to the water.
  • Use a sponge or flannel to thoroughly clean the infected area. Make sure you soak the affected area ONLY - do not allow your rabbit or guinea pig to get completely wet.
  • Some maggots may fall off during cleaning. Carefully remove any remaining maggots with tweezers.
  • Once you’ve removed ALL the maggots, dry your rabbit or guinea pig. You can do this by gently patting them with a towel.
  • Once your pet is warm and dry, apply a vet strength medicine containing ivermectin, such as Beaphar Fly Guard, to kill any maggots that may hatch from any remaining eggs. Be sure to follow the application instructions.
  • Clean out and disinfect your rabbit or guinea pig’s hutch or cage. Be sure to remove any faeces, and thoroughly clean and soiled areas that could attract more flies. Replace all the bedding and litter trays/areas with fresh bedding and litter.
  • Continue to check your rabbit or guinea pig at least twice a day (or as directed by your vet) and clean if necessary. Check your other rabbits or guinea pigs too, even if they don’t appear to have been ‘struck’, and apply Beaphar Fly Guard.
  • Spot clean your pet’s toilet area or litter tray 1–2 times a day to remove faeces and reduce the attraction of flies.
  • Seek veterinary attention immediately. If you’ve treated your pet with Beaphar Fly Guard or a similar product, take the product and packaging with you. This will allow your vet to treat your pet more appropriately.

How can I prevent my rabbits or guinea pigs from getting fly strike?

Some flies produce maggots that start feeding within 24 hours, so fly strike prevention is essential. The best way to prevent your rabbits or guinea pigs from getting fly strike is to maintain good hygiene.

If you prepare for fly strike and prevent flies being attracted to your pets' home, you can easily protect them from fly strike.

Step 1


  • Ensure your rabbits or guinea pigs are receiving a good diet
  • Incorrect nutrition will impact your pets’ digestion. This can lead to diarrhoea or softer faeces, which can get caught around the bottom. A pelleted, high fibre diet with plenty of clean hay and access to grass will mean a healthy diet and cleaner bottom. Find out more about rabbit nutrition here.
  • Beaphar Deep Clean Disinfectant
  • Completely clean your pets’ cage or hutch every week
  • Remove all bedding and disinfect your pets’ hutch or cage with Beaphar Deep Clean Disinfectant . This will remove any dirt that may attract flies and kill any harmful viruses and bacteria that may be lurking.
  • Locate the toilet area or litter train your pet
  • Knowing where your pets like to do their business will make it easier for you to spot clean. Rabbits can be litter trained, making spot cleaning even easier.
  • Invest in a suitable animal shampoo, comb and scissors
  • All pets need grooming, but if your rabbits or guinea pigs get a messy bottom, you want to make sure you have the right tools. Beaphar Guinea Pig and Rabbit Shampoo is gentle but effective, and specifically for small animals. Ideally, faeces should be cleaned and combed out. Heavily matted fur may need to be carefully cut away with scissors.
  • Older, overweight or longer haired pets may find it harder to clean themselves, so are more likely to need intervention. Check all pets daily for signs of fly strike. Check pets that fall into these categories more frequently; a minimum of twice a day.


Step 2


  • Beaphar Cage Fresh GranulesClean the toilet area daily
  • We recommend using Beaphar Deep Clean Disinfectant to disinfect the area and remove harmful germs and bacteria. For stubborn dirt, debris and areas of heavy soiling, use Beaphar Hutch & Cage Cleaner first. You can then use Beaphar Deep Clean Disinfectant to disinfect the area.
  • Before replacing the litter, you can also use a sprinkle of Beaphar Cage Fresh Granules. The granules contain friendly-microbes which break down the odours of urine, helping to reduce the attraction of flies and risk of fly strike. If you wish, Beaphar Cage Fresh Granules can be used throughout your pets’ home as well.
  • Check your pets’ bottoms daily and clean if necessary
  • Rabbits and guinea pigs are both sociable creatures, so it’s important to interact with them every day. During this bonding time, you can check your pet’s bottom and back end.
  • Carefully clean and comb out any faeces. Clip out any stubborn, matted fur, ensuring you don’t hurt your pet. Once your pets’ bottom is clean, dry the area thoroughly.
  • In the summer months you may wish to check your pets 2–3 times a day. Keeping your pets’ bottoms clean will reduce the risk of fly strike.
  • Feed an appropriate diet
  • Continue to monitor your pets’ diet, ensuring they are receiving the correct nutrition. This will help keep their digestive system healthy and reduce the chance of diarrhoea or soft faeces.


Step 3


  • Beaphar Fly GuardTreat your rabbits or guinea pigs with Beaphar Fly Guard
  • A vet strength medicine that contains ivermectin and kills maggots before they can cause damage. One application protects your pets from fly strike for up to three months.
  • Maintain excellent hygiene practices
  • Continue to clean and disinfect your pets’ toilet area and their hutch or cage as directed. Also continue to check your pets’ bottom and clean as required.
  • Keeping your pets and their environment clean will reduce the attraction of flies, helping to prevent fly strike.
  • Reapply Beaphar Fly Guard at the recommended intervals
  • To ensure complete protection for your rabbit or guinea pig, be sure to reapply Beaphar Fly Guard every three months. Any gap in treatment may allow fly strike to develop.