BACKGROUND Clear cell sarcoma is an aggressive rare malignant neoplasm with morphologic and immunohistochemical similarities to malignant melanoma. Both disease entities display melanin pigment and melanocytic markers, making differentiation between the two difficult. Although clear cell sarcoma cases in the literature have mainly involved deep soft tissues of the extremities, trunk or limb girdles, we report here two cases of primary clear cell sarcoma in unusual sites and describe their clinicopathologic findings. METHODS The first case involves a 37-year-old female, who presented with jaw pain and a submandibular mass. The second case involves a 33-year-old male, who presented with back pain and a thoracic spine tumor. Both cases showed tumors with diffuse infiltration of neoplastic cells that were positive for melanocytic markers, and in both cases this finding led to an initial diagnosis of metastatic melanoma. However, further analysis by fluorescence in situ hybridization (commonly known as FISH) showed a rearrangement of the EWS RNA binding protein 1 (EWSR1) gene on chromosome 22q12 in both patients, confirming the diagnosis of clear cell sarcoma. CONCLUSIONS Distinction between clear cell sarcoma and malignant melanoma can be made by FISH, particularly in cases of unusual tumor sites.