Methicillin resistant Staphylococcus aureus (MRSA) strains lead to severe infections in immunosupressive patients, geriatric population and premature infants. 27 MRSA strains isolated in the Neonatal Intensive Care Unit was considered as an outbreak and it was aimed to investigate the genetic and epidemiologic relation of the MRSA outbreak. MecA gene was investigated in the S. aureus strains and pulsed field gel electrophoresis (PFGE) was used to investigate the genetic relation between outbreak strains. MecA gene was showed in all isolates. PFGE revealed that there were two different strains and most of the isolates (25/27) were owing to same clone. One of the samples were found closely related with the common strain and the other sample was found genetically unrelated. To terminate the outbreak; liquid baby food was gained to the baby food kitchen, no more new patient was imported to the neonatal unit and none of the patients were exported from neonatal unit to other clinics during outbreak, education about infection control precautions was given to all the staff and nursing bottle dishwasher was obtained. To manage and terminate the outbreak, besides the infection control precautions, tests to determine the genetic relation between outbreak strains which are done in the microbiology laboratory are needed. Molecular analysis of outbreak strains will contribute to prove the epidemiologic and evolution of outbreaks