Allergy is caused by the immune system over-reacting to substances in drugs, food and the environment. It can occur at any stage of HIV infection; this may seem paradoxical in a disease where the immune system is damaged, but allergy probably occurs because the normal controls on the immune system are not working correctly.

Asthma is an example of a disorder which may have an allergic component. It is thought that environmental substances may trigger off difficulty in breathing.

People with HIV seem to be more prone to drug allergy than uninfected people. Allergy to co-trimoxazole is often seen during treatment for Pneumocystis pneumonia (PCP). This can result in rashes and high fevers.