Methicillin-resistant Staphylococcus aureus (MRSA) is a global threat to public health. This study is the first report of the emergence of vancomycin-resistant MRSA in Kerman, Iran. During a period of 15 months, a total of 205 clinical isolates of S. aureus were collected from three university hospitals affiliated with the Kerman University of Medical Science, Kerman, Iran. Screening of methicillin and vancomycin resistance was carried out by phenotypic methods. The resistance and virulence genes of vancomycin-resistant isolates were detected by polymerase chain reaction (PCR). Staphylococcal cassette chromosome mec (SCCmec) and spa typing were used for molecular typing of vancomycin-resistant isolates. Two S. aureus isolates were considered vancomycin-resistant by phenotypic and genotypic methods. Both isolates showed a minimum inhibitory concentration (MIC) ≥ 64 µg/ml and belonged to SCCmec III and spa type t030. Finding vancomycin-resistant S. aureus (VRSA) isolates represents a serious problem. More stringent infection control policies are recommended to prevent transmission of such life-threatening isolates in the hospital setting.