Microbiological diagnosis of extrapulmonary tuberculosis [EPTB] is based on microscopy, culture and molecular tests. A prospective study was done to determine sensitivity and specificity of Xpert MTB/RIF assay and LED fluorescent microscopy in clinically suspected cases of EPTB in comparison with solid culture. Consecutive 275 extrapulmonary specimens were mainly pleural fluid (5.81%) followed by CSF (36.2%), pus (37.5%) and lymph node biopsy (40.90%). ZN and LED microscopy, Xpert assay and culture detected 14, 19, 59 and 70 cases respectively. LED microscopy and Xpert assay had sensitivity and specificity of 27.14%; 100% and 80%;98% respectively. Xpert assay detected MTB in 59 (21.45%) specimens with 22.03% rifampicin resistance. 17 specimens showed discordant results. Xpert MTB/RIF assay is a rapid and time–saving diagnostic test and should be used as the initial diagnostic test for detection of tuberculosis as well as rifampicin resistance in all EPTB. LED microscopy should replace ZN microscopy.