Scratching Scratching is also normal for guinea pigs, though excessive scratching can be a sign of a parasitic infection, such as lice or mites. Less common are fungal infections, which can also cause hair loss. Often times, it will take two baths, about a week or two apart, to completely eradicate lice from a guinea pig. The first bath kills the existing lice, and the second kills the lice that hatch from the first batch's eggs. You can obtain a pyrethrin shampoo from your vet, who will instruct you in its use.
Mites are more difficult to kill.
They are also hard to spot initially, as they can't be seen with the naked eye. There are some home-remedies for eliminating mites, but most people opt for veterinary care, which usually involves injections of Ivermectin. Contrary to popular belief, fleas are not a big problem with guinea pigs. For some reason, fleas don't care much for the species, and usually aren't present for very long if they do take up residence. The hutch should always be cleaned and disinfected when dealing with parasites.