The drug resistance of Mycobacterium tuberculosis (MbT) remains a serious challenge to global public health as extensively drug resistant tuberculosis usually leads to a lethal outcome. In the case of diseases with resistant strains, it is extremely important to identify a specific strain as soon as possible in order to start an adequate therapy. One such diagnostic method could be the Raman spectroscopy method. We investigated M. tuberculosis strains of the Beijing family deactivated by heating, with different drug sensitivity: sensitive, multi- and extensively drug resistant. Samples, obtained from patient specimens were investigated by Raman spectrometry with the He–Ne (632.8 nm) laser excitation source. As a result, a set of optimal experimental parameters for strain discrimination were determined based on the cell-wall spectral differences. These differences distinguish between drug-sensitive and drug-resistant strains as well as between strains isolated from material samples taken from patients suffering from pulmonary and extra-pulmonary forms of tuberculosis. We suggest that the obtained results allow the usage of the Raman spectroscopy as a fast diagnostic tool for determining various strains in clinical medical practice.