Clear cell odontogenic carcinomas (CCOCs) are a rare tumor of the jaws, which have considerable morphologic and immunophenotypic overlap with (hyalinizing) clear cell carcinomas (CCCs) of salivary origin. Fluorescence in situ hybridization for EWSR1 was performed on 12 CCOCs, 14 CCCs, and a control set of other miscellaneous clear cell tumors of the head and neck region. EWSR1 was rearranged in 12/13 (92.3%) CCCs and 5/8 (62.5%) CCOCs. EWSR1 testing failed in 1 CCC and 4 CCOCs. Two cases initially diagnosed as CCOCs that were negative for the EWSR1 translocation, were reclassified as clear cell calcifying epithelial odontogenic tumors. ATF1 involvement was confirmed by fluorescence in situ hybridization analysis in 1 CCOC. In this study, we demonstrate for the first time the EWSR1-ATF1 translocation in a CCOC and demonstrate a concrete link between CCCs and at least a subset of CCOCs.