primordial cyst primordial cyst a primordial cyst is a developmental odontogenic cyst. it is found in an area where a tooth should have formed but is missing. primordial cysts most commonly arise in the area of mandibular third molars. under microscopes, the cyst looks like an odontogenic keratocyst (also called a keratocyst odontogenic tumor) whereby the lesions displays a parakeratinized epithelium with palisading basal epithelial cells. the term "primordial cyst" is considered an outdated term and should be avoided. most "primordial cysts" are actually keratocyst odontogenic tumors (kot's).