Angiomatoid fibrous histiocytoma is a mesenchymal neoplasm of intermediate malignancy and uncertain histogenesis/line of differentiation, which occurs most commonly in the extremities of children to young adults. It has a characteristic appearance characterized by a proliferation of histiocytoid cells with a lymphoid cuff and fibrous pseudocapsule, simulating the appearance of a neoplasm occurring within a lymph node. However, these classic histological features are not always present. Given the variable appearance of the neoplastic cells and the lack of consistently positive immunohistochemical markers, diagnosis can be problematic. Angiomatoid fibrous histiocytoma has been found to harbor three related translocations, a t(12;16)(q13;p11) resulting in a FUS/ATF1 fusion gene, t(12;22)(q13;q12) resulting in a EWSR1/ATF1 fusion, and t(2;22)(q33;q12) resulting in a EWSR1/CREB1 fusion. Fluorescence in situ hybridization (FISH) probes to EWSR1 and FUS, in theory, should detect all three translocations/gene fusions. We evaluated 18 cases of angiomatoid fibrous histiocytoma for rearrangements of EWSR1 and FUS by FISH, the largest series to date. We found that 13 of 17 (76%) cases of angiomatoid fibrous histiocytoma harbored rearrangements of EWSR1; rearrangements of FUS were not detected in any of the cases. This study affirms that the rearrangement of EWSR1 is a common genetic event in angiomatoid fibrous histiocytoma, and is thus useful diagnostically. This study supports the fact that the rearrangement of FUS is present in only a small minority of angiomatoid fibrous histiocytomas. Interestingly, 24% of the cases were translocation negative, and did not contain rearrangements of EWSR1 or FUS by FISH. Although it is possible that these cases contained cryptic rearrangements of EWSR1 or FUS that were not detectable by our FISH probes, it also raises the possibility that another translocation/gene fusion may be present in angiomatoid fibrous histiocytoma. Finally, we discuss some of the potential pitfalls of this technique, including confusion with other mesenchymal neoplasms containing rearrangement of EWSR1, in particular Ewing's sarcoma/PNET.