[3] The AAEM has been cited as an questionable organization by Quackwatch for promoting discredited diagnoses like multiple chemical sensitivity, chronic candidiasis, and toxic mold syndrome.

Members of the academy may have a background in the field of allergy, and their theoretical approach is derived in part from non-standard concepts of allergic responses that were first articulated by Randolph in the 1960s.

The AAEM works towards the greater recognition, treatment and prevention of illnesses induced by exposures to various biological and chemical agents encountered in our environment, such as in air, food and water.

Proponents of clinical ecology may claim cause-and-effect relationships or low-dose effects that are not generally accepted by toxicologists (allergy, immunology and toxicology).

Randolph's theories about how allergies happen, which he promoted from the founding of the field, are the original basis for the suspicious attitude of mainstream medical, legal, and scientific experts towards clinical ecology as a whole.