Specific Disease Protocol:
Antihistamines and Allergies
In the case of severe allergies, the FAA requires that the AME deny or defer certification and provide a report to the Aerospace Medical Certification Division, AAM-300, that details the period and duration of symptoms and the nature and dosage of drugs used for treatment and/or prevention.
Severe is the operative word in the FAA's guidance. The classification of "severe" is a judgment call that will be made after a discussion between the pilot and the AME. Find and AME. Aeromedical factors to consider include requirement for antihistamines (these medications often have sedating side effects which are incompatible with piloting or controlling duties).
Physiologically speaking, allergies may cause the ventilating passages for the middle ear and sinuses to become obstructed, and this can lead to a debilitating and painful situation during ascent or descent due to changes in cabin pressure which cannot equilibrate with the trapped air cavities in the sinuses or middle ear. See Ear section of Medical Standards (CFR Part 67) for Class 1, for Class 2, for Class 3.