Introduction: Tuberculosis (TB) remains a deadly infectious disease despite all the efforts to reduce its incidence. Spread of multidrug resistant TB has seriously undermined the efforts to control the disease globally. In this study protein expression profile of MDR and sensitive isolates of MTB were analyzed and compared in order to identify proteins, which could be used in prevention, diagnosis and treatment. Methods: A sensitive and MDR isolate of Mycobacterium tuberculosis (MTB) were cultured on Middlebrook 7H9 medium and the whole cell lysates were subjected to native polyacrylamide gel electrophoresis (NPAGE) for protein expression profiling. Protein bands present in the MDR cell lysate that were not detected in the sensitive cell lysate were sent for identification by Matrix-assisted laser desorption/ionization time-of-flightmass spectrometry (MALDI-TOF-MS). Results: Comparison of the protein expression profiles showed 6 bands that were not detected in the sensitive isolates. MTB Structural Annotation database search of the mass spectrometry results identified these bands as Rv3597c, Rv0379,Rv3614c, Rv0475, Rv0462, andRv0147and global transcriptional regulation, involvement in cell wall and cell processes and intermediary metabolism and respiration were the functions attributed to these proteins. Conclusion: Our results highlighted the complexities of linking protein expression to MDR phenotype as none of the proteins identified could be linked directly to drug resistance. The proteins identified in the present study were mostly those essential for survival or virulence of the bacteria, and could be used for diagnosis or as candidate vaccine, but with a better understanding of the function of these proteins their association with the MTB resistance to antibiotics might become clear.