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The performance of the GeneXpert MTB/RIF assay for the diagnosis of extrapulmonary tuberculosis (TBEP) has not been investigated in Panama. The objective of the study was to evaluate the diagnostic accuracy of the GeneXpert MTB/RIF assay for various extrapulmonary samples relative to the reference method: MGIT/LJ (Mycobacteria Growth Indicator Tube/Lowenstein-Jensen) culture. A total of 200 clinical samples was obtained and tested for TBEP using the GeneXpert MTB/RIF assay and standard conventional methods (culture and direct smear). The sensitivity (S), specificity (E), positive predictive value (PPV), and negative predictive value (NPV) of the Xpert MTB/RIF assay for TBEP were 66.6%, 97.3%, 66.6, and 97.3%, respectively. The GeneXpert MTB/RIF assay was found to have good specificity, but its sensitivity is variable and will depend on the type of sample used. We conclude that the GeneXpert MTB/RIF represents a good tool for the diagnosis of TBEP, but a negative result will not rule out the disease. Therefore, it cannot be recommended to replace standard conventional tests for the diagnosis of TBEP, however, its use together with traditional methodologies improves diagnosis.