BACKGROUND: Extrapulmonary TB (EPTB) comprises approximately 15–20% of TB cases worldwide, and its diagnosis is difficult. The sensitivity of Xpert® MTB/RIF (Xpert) in the diagnosis of EPTB is low on account of its paucibacillary nature. Xpert® MTB/RIF Ultra (Ultra) was developed to improve sensitivity.OBJECTIVE: To compare the sensitivity of Ultra test with that of Xpert against MGIT™ (Mycobacteria Growth Indicator Tube) culture and a composite reference standard (CRS).METHODS: We recruited consecutive treatment-naïve patients with suspected EPTB. Demographic information, clinical and relevant laboratory data were collected.RESULTS: From January 2019 to November 2019, 210 patients provided 250 samples. Against MGIT culture, the sensitivity of Ultra was significantly higher than Xpert (72% vs. 51.1%; P = 0.04), the specificity was lower (87.8% vs. 95.1%). Against the CRS also, the sensitivity of Ultra was significantly higher than Xpert (45.4% vs. 25.2%; P = 0.002); however, the specificities were similar (98.2% vs. 99.1%). The trend towards higher sensitivity of Ultra compared to Xpert was seen in most of the individual samples. The sensitivities against MGIT and CRS were as follows: lymph node (68.1% vs. 31.8%; P = 0.01) and (59.5% vs. 23.8%; P = 0.001), pleural biopsy (80.0% on both; P = NS) and (53.8% vs. 46.2%; P = NS) and pleural fluid (66.7% vs. 50%; P = NS) and (22.5% vs. 9.6%; P = NS), respectively.CONCLUSIONS: Xpert Ultra showed a significantly higher sensitivity in diagnosing EPTB than Xpert.