According to PetMD, one of the most common causes for hair loss in guinea pigs is barbering, an instinctual behavior in which guinea pigs chew off their own hair or the hair of other guinea pigs during conflict. Female guinea pigs also engage in barbering behavior when under stress.
VeterinaryPartner.com explains that in addition to barbering, external parasites are a common culprit for hair loss in guinea pigs. Lice and mite infestations cause severe itching and scratching which leads to hair loss and crusting of the skin. In severe cases, intense scratching and discomfort can lead to deep skin injuries and wild circling behavior. Lice and mites are treated with anti-parasitic drugs at two week intervals until the infestation is eradicated.