Studies evaluating the new GeneXpert Ultra with other rapid diagnostic assays are limited, particularly in different geographical settings. The performance of the GeneXpert Ultra, the GeneXpert G4, the Line probe assays (LPA) and auramine smear microscopy in detecting TB in pulmonary and extra-pulmonary samples were thus evaluated. Remnants (n = 205 samples) of pulmonary (n = 125 samples) and extra-pulmonary (n = 80 samples) specimens from TB suspects were prospectively collected. Each sample was divided for diagnosis using microscopy, GeneXpert MTB/RIF assays, and LPA; these were all comparatively evaluated, using the MGIT 960 culture as a gold standard. The sensitivity and specificity of microscopy, Xpert Ultra, Xpert G4 and MTBDRplus (ver 2) in pulmonary samples were respectively: 82.00% and 90.28%; 88.00% and 58.57%; 79.59% and 90.28%; 80.00% and 11.11%. For extra-pulmonary specimen, the sensitivity and specificity were respectively: 53.85% and 98.51%; 69.23% and 49.25%; 50.00% and 97.01%; 69.23% and 25.37%. The new and improved GeneXpert Ultra assay was more sensitive than GeneXpert G4 and LPA in both pulmonary and extra pulmonary samples, albeit with lower specificity than the GeneXpert G4. The auramine and LPA tests were also highly sensitive, although the LPA was less specific.