This case-sensitive code system http://hl7.org/fhir/allergy-intolerance-type defines the following codes:
Code
Display
Definition
allergy
Allergy
A propensity for hypersensitive reaction(s) to a substance. These reactions are most typically type I hypersensitivity, plus other "allergy-like" reactions, including pseudoallergy.
intolerance
Intolerance
A propensity for adverse reactions to a substance that is not judged to be allergic or "allergy-like". These reactions are typically (but not necessarily) non-immune. They are to some degree idiosyncratic and/or patient-specific (i.e. are not a reaction that is expected to occur with most or all patients given similar circumstances).