The correct choice of antibiotics is especially important in guinea pigs because of the danger of inducing changes in the intestinal microbial flora and, consequently, fatal enteritis. Narrow-spectrum antibiotics are the most dangerous; some, such as penicillins and lincosamides, are absolutely contraindicated; others, such as tetracyclines, are potentially dangerous and should only be used when really necessary and with caution, suspending administration at the first signs of changes in the faeces. Streptomycin, dihydrostreptomycin and products containing procaine should never be used because they cause immediate death from direct toxic effects due to neuromuscular block.

Sensible choices must also be made regarding topical treatment, because guinea pigs lick themselves which leads to the ingestion of locally applied drugs. Drugs considered safe for topical use include sulphadiazine and chlorhexidine which, even when ingested in small amounts, do not involve risks of disordered intestinal microbial flora. It is a good idea to clip the hair before applying drugs to the skin and use the minimum required dose of the product. Do not apply greasy substances, to avoid getting the animal dirty.
Guinea pigs easily become stressed; this condition can be made worse by hospitalisation. It is preferable to treat a guinea pig at home but, when necessary, the stress of hospitalisation can be considerably reduced by keeping the rodent in its cage with its companions and placing it in as peaceful an environment as possible, where there are no potential predators (dogs, cats, ferrets) or loud noises.
Sick guinea pigs always require vitamin C supplementation and, in the case of painful conditions, it is essential to provide suitable pain-relieving treatment. Guinea pigs are not very combative animals, and easily let themselves go under pathological conditions; care and attention, such as stroking and petting and offering food that they like, can improve their response to treatment.