Endometrial stromal tumors (ESTs), including low-grade endometrial stromal sarcomas (LGESSs) and endometrial stromal nodules (ESNs) of classic histology, exhibit characteristic morphologic features and contain the nonrandom t(7;17)(p15; q21), which results in the fusion of two novel genes, JAZF1 and JJAZ1. ESTs may pose diagnostic challenges when they involve extrauterine sites, present as metastases, or display variant histologic appearances. The aim of this study was to evaluate the frequency of the JAZF1-JJAZ1 gene fusion among primary uterine, metastatic, and primary extrauterine ESTs of various histologic types and its role as a possible diagnostic adjunct. Using a nonnested reverse transcriptase-polymerase chain reaction approach, we assayed for JAZF1-JJAZ1 gene fusion transcripts in 10 cases with available fresh-frozen tissue. These included five primary uterine (two classic, one mixed smooth muscle, and one epithelioid LGESS; one classic ESN), four metastatic (two fibromyxoid, one classic, and one epithelioid LGESS), and one extrauterine (classic LGESS) tumor. The same primer set and assay conditions were used on five additional paraffin-embedded cases with adequate RNA, including three primary uterine (one fibromyxoid and one mixed smooth muscle LGESS; 1 mixed smooth muscle ESN) and two intraabdominal recurrent (two mixed smooth muscle LGESSs) ESTs. Two cellular leiomyomas and one ESS cell line (ESS-1) without the t(7;17) at the cytogenetic level were run in parallel as controls. JAZF1-JJAZ1 gene fusion transcripts were detected in five (33%) of 15 ESTs, including three of eight primary uterine, one of four metastatic, one of one extrauterine, and none of two recurrent cases. Most ESTs of classic histology showed evidence of JAZF1-JJAZ1 fusion (4 of 5 cases), whereas only one mixed smooth muscle ESN of 10 variant cases was positive. Positivity for JAZF1-JJAZ1 fusion transcripts was found in four of 10 fresh-frozen samples and in one of five paraffin-embedded ESTs. The control specimens were all negative. In conclusion, our data suggest that ESTs are genetically heterogeneous, with the prevalence of the JAZF1-JJAZ1 fusion being highest among ESTs of classic histology. Hence, the diagnostic utility of a JAZF1-JJAZ1 fusion transcript assay in ESTs may be limited to the classic histologic subset.