Introduction: Infections by multidrug resistant Mycobacterium tuberculosis (MDR-TB) is a major public health challenge. Secretion of proteins by M. tuberculosis plays an important role in the pathogenesis of the bacterium. We compared the protein profiles of susceptible M. tuberculosis and MDR-TB isolates using proteomic analyses, namely two dimensional gel electrophoresis (2DE) and mass spectrometry (MS). Methods: The bacilli were cultured on Middlebrook 7H9 medium and bacterial colonies were mechanically disrupted and proteins were extracted by ammonium sulfate. The 2DE and MS analyses were performed using Ettan IP Gphor 3 isoelecteric system and Autoflex II TOF/TOF, respectively. Results: Our study showed that in comparison to the sensitive strains, 27 proteins were over-expressed in the MDR isolates and these proteins were mainly involved in the cellular metabolism, cell wall and membrane structures and bacterial respiration. Bactoferritin (Rv1876) has been shown to play a role in antibacterial resistance. Increased intensity of Rv2031c, a heat shock protein (Alpha-crystallin/HspX), was also observed in the whole cell lysate of the MDR-TB. This protein is a marker of the latent TB and has been proposed as a target for vaccine development. Conclusion: Our results identified proteins that are overexpressed in the resistant M. tuberculosis which could be used as antibacterial targets or vaccine candidates.