The odontogenic keratocyst (OKC) is a cystic lesion, lined by uniformly thickened parakeratinized epithelium. Some lesions are large and tend to recur after surgical treatment. The neoplastic nature of OKCs remains a matter of dispute. It is known that some sporadic OKCs harbor PTCH1 mutations, and via the dissection of cyst epithelium, these mutations were demonstrated to occur much more frequently than previously thought. In addition to the classical PTCH1 mutations, Hedgehog pathway disturbance and Bcl-2 protein overexpression, as detected via genome-wide expression analysis of OKCs, have been published. Changes in DNA methylation patterns and alterations in microRNA expression levels have recently been reported in these lesions. We reviewed the molecular mechanisms that underlie the pathogenesis of OKCs as described over the past few years and explored the molecular alterations that can be therapeutically targeted.