The MTBDRplus line probe assay (LPA) and Xpert MTB/RIF have been endorsed by the World Health Organization for the rapid diagnosis of drug-resistant tuberculosis. However, there is no clarity regarding the superiority of one over the other. In a double-blinded prospective study, we evaluated the efficacy of the Xpert MTB/RIF on samples that were first tested by LPA under the revised national tuberculosis control program of India. A total of 405 sputum samples from suspected drug-resistant tuberculosis patients were included. Of these, 285 smear-positive samples were subjected to LPA. Seventy-two (25.8%) samples showed multidrug resistance, 62 (22.2%) showed rifampin monoresistance, 29 (10.3%) showed isoniazid monoresistance, and 116 (41.5%) were pan-susceptible. Six (2.1%) of the samples gave invalid results. Of the 62 rifampin-monoresistant samples by LPA, 38 (61.4%) showed rifampin resistance, while 21 (33.8%) were found susceptible to rifampin by Xpert MTB/RIF using cartridge version G4. Three (4.8%) samples gave an error. Of the 116 pan-susceptible samples, only 83 were available for Xpert MTB/RIF testing; 4 (5.1%) were rifampin resistant, 74 (94.8%) were susceptible, and 5 (6.0%) showed an error. The 25 discrepant samples were further subjected to MGIT960 drug susceptibility testing. The MGIT960 results showed 100% agreement with LPA results but only 64.4% agreement with Xpert MTB/RIF results. Sequencing analysis of discrepant samples showed 91.3% concordance with LPA but only 8.7% concordance with the Xpert MTB/RIF assay. These findings indicate that by using Xpert MTB/RIF testing we might be underestimating the burden of drug-resistant tuberculosis and indicate that country-specific probes need to be designed to increase the sensitivity of the Xpert MTB/RIF. T he global burden of tuberculosis (TB), particularly with multidrug resistance (MDR), is increasing and has become a major health challenge (1). The disease caused by Mycobacterium tuberculosis resistant to two primary antitubercular drugs, rifampin (RIF) and isoniazid (INH), is known as MDR-TB. Such instances are more common among clinical relapse cases (2). It has been reported that M. tuberculosis that is resistant to RIF is more likely to have concomitant resistance to INH, making RIF resistance a surrogate marker of MDR-TB (3). Early diagnosis of TB and rapid detection of RIF resistance is important for proper management of drug-resistant TB (DR-TB) (4). But in spite of major efforts that are being done to increase case detection, one-third of new TB cases are still missed due to nonavailability of rapid, low-cost, and accurate diagnostic facilities in high-TB-burden countries (5).Over the last 6 years, efforts have been made to improve and develop rapid diagnostic tools and drug susceptibility testing (DST) for TB. During this period, the World Health Organization (WHO) had issued 10 policy statements for improving diagnosis of TB, including the use of commercial and noncommercial DST methods and implementation of molecular methods such as the ...