The present investigation aims to find a specific method to test the clinical isolates of Staphylococcus aureus in terms of antimicrobial susceptibility and resistance to two drugs of cefalotin and vancomycin using E-test and Disk Diffusion methods. Totally 80 samples were collected from hospitalized patients at the general hospitals of Kerman Province, Southeastern, Iran between November 2013 to April 2014. They were identified by standard microbiological methods. Susceptibility by Disk diffusion and MIC by E-test were performed according to the Clinical and Laboratory Standards Institute breakpoints. In the disk diffusion method for vancomycin antibiotic, the S. aureus specimens were reported to be 15% resistant, 27% intermediate, and only 38% susceptible. Also, for cefalotin antibiotic, the specimens were reported as 48% resistant, 19% intermediate, and only 13% susceptible. In the E-test method for vancomycin antibiotic, the S. aureus specimens were reported to be 29% resistant, 18% intermediate, and 33% susceptible. Also, for cefalotin, the specimens were reported to be 59% resistant, 11% intermediate, and 10% susceptible. By statistical comparison using SPSS software and Chi Square test, the P-value of 0.001 was obtained; therefore, regarding the zero hypothesis, there is a significant relationship between these two methods of microbial susceptibility determination at (p <0.05), and accept that the E-test method is still a suitable test for susceptibility determination for this bacterium. The findings of present study revealed the high resistance of this bacterium in Kerman Province and feeling the necessity of thinking of some strategies and solutions for reducing that microbial resistance as well as paying more attention to the selective treatments, antibiotic treatment course duration, and other instances that should be taken into account in any antibiotic diet in order to prevent and avoid such high levels of microbial resistance in our country.