Simple preventive measures can help avoid hair loss in guinea pigs. Freezing hay, pellets, and bedding before use will eliminate mites and lice that cause itching and hair loss.
Learn how to manage hay allergies as a guinea pig owner, from identifying symptoms to practical strategies that let you keep your beloved pets despite allergic reactions.

Both patients report symptoms with guinea pig exposure with negative skin testing to guinea pig and marked sensitivity to Timothy grass, a component of the guinea pig diet. Symptoms are determined to be due to Timothy grass pollen exposure.

Feeding your guinea pig low-quality hay can cause nutritional deficiencies, leading to a dull coat, dry skin, and hair loss. It can also result in dental problems and digestive issues, which compromise overall health.
My guinea pig has a bit of isolated hair loss. The skin there looks perfectly healthy though. Could it be caused by her hay fever? Kind of in the same way...