Extraskeletal myxoid chondrosarcomas (EMC) are rare soft tissue sarcomas with distinctive histology and uncertain histogenesis, characterized by EWSR1-NR4A3 fusion in 75% of the cases. A smaller proportion of cases show NR4A3 fused to other gene partners including TAF15, TCF12 and TFG. The impact of various gene fusions on morphology and outcome has not been previously evaluated. We investigated 26 consecutive EMCs and correlated the genetic findings with morphology and clinical outcome. There were 5 females and 21 males (median age of 49.5 years). Mean size of the tumors was 11 cm. FISH analysis showed EWSR1-NR4A3 gene fusion in 16 (62%) cases; TAF15-NR4A3 gene fusion in 7 (27%) cases and TCF12-NR4A3 gene fusion in one (4%) case. Two cases showed only NR4A3 gene rearrangements. Morphologically, most EWSR1-rearranged tumors (10 of 16) showed low cellularity, minimal cytologic atypia and low mitotic counts. In contrast, 80% of EMCs with variant (non-EWSR1) NR4A3 gene fusions (TAF15, TCF12) had high grade morphology with increased cellularity, proliferation and cytologic atypia, showing a plasmacytoid / rhabdoid morphology in half the cases. Follow-up showed that only 1 of 16 patients with EWSR1-rearranged tumors died of disease, in contrast to 3 of 7 (43%) TAF15–rearranged tumors. In conclusion, EMCs with variant NR4A3 gene fusions show a higher incidence of rhabdoid phenotype, high grade morphology and, a more aggressive outcome compared to the EWSR1-NR4A3 positive tumors. Furthermore, FISH assay for NR4A3, along with EWSR1, may be an additional ancillary test to confirm diagnosis of EMCs.