Half a million new cases of multidrug-resistant tuberculosis (MDR-TB) are registered annually, and therefore, the issue of the development of new fast and reliable methods for diagnosis of tuberculosis (TB) remains urgent in modern phthisiology. The aim of this study was to investigate the effects of the Xpert MTB/RIF molecular genetic method on the diagnosis, clinical and radiological features, and efficacy of treatment of MDR-TB. Patients with MDR-TB were divided into two groups. The first (study) group included patients ( = 412) in whom a mutation in the gene responsible for the presence of () and resistance to rifampicin were detected using the Xpert MTB/RIF assay. The second group consisted of patients ( = 540) in whom TB was diagnosed using bacterioscopy and multidrug resistance was detected using inoculation on dense and liquid culture media. The results of bacterioscopic, bacteriological, molecular genetic, clinical studies and the efficacy of the treatment of 952 patients with MDR pulmonary TB were studied. The result of GeneXpert MTB/RIF was compared with the results of sputum bacterioscopy and culture methods on a dense Levenshtein-Jensen nutrient medium and on a liquid nutrient medium in a BACTEC 960 automated microbiological system. The "Successful treatment" outcome ("cured" and "treatment completed") prevailed among patients who underwent timely diagnosis of MDR-TB using the Xpert MTB/RIF assay and reached 73.8%. In the second group of patients, it was 49.3% ( = 0.000). Timely diagnosis of MDR-TB using the Xpert MTB/RIF assay increased the efficacy of anti-TB chemotherapy.