A rare case of primary intraosseous squamous cell carcinoma arising in an odontogenic keratocyst (OKC) is presented here, with the clinical and histologic features of the first biopsy showing characteristics of OKC and the second biopsy disclosing a squamous cell carcinoma. Immunoprofile of this case was compared with five cases of classical OKC by using cytokeratins CK5, CK14, and CK19, CD138, p63, Ki-67, p53, and bcl-2. Classic OKCs showed expected positivity, mainly in the basal and/or suprabasal layers with most antibodies, except for p53, which was negative, whereas the present case showed irregular positivity in all layers, indicating that this can be useful for differential diagnosis and suggesting a possible role in malignant transformation into primary intraosseous squamous cell carcinoma. In conclusion, immunohistochemical differences between the first biopsy of the present case and classic OKC suggest that immunohistochemistry can be helpful in cases with areas of subtle initial malignant transformation.