BACKGROUND: Staphylococcus aureus is one of the most important human pathogens that cause infection and also food intoxication by secreting various enterotoxins. Conventional culturing methods to detect S. aureus have some limitations such as being time-consuming due to bacterial growth and low precision and sensitivity in detecting viable but non-cultivable cells. OBJECTIVES: The objective of this study was to detect and quantify enterotoxigenic (A-E) S. aureus in cream pastry products applying PCR coupling with propidium monoazide (PMA) to distinguish dead and live cells. METHODS: One hundred samples were randomly collected from pastry shops in Amol, in a period of 2 months. After preparing dilutions, bacterial pellets were separated and treated with PMA before DNA extraction. Real time PCR was conducted in order to quantify S.aureus cells and enterotoxigenic strains using specific primers. RESULTS: Results of conventional method were close to PMA-qPCR data (P>0.05), but data from qPCR that includes live and dead cells shows more bacterial count than two other methods. Sensitivity of the method applied in the present study, detecting low number of S.aureus cells (less than 10/g) seems considerable. CONCLUSIONS: Findings showed that applying PCR coupling with PMA results in more reliable data than conventional culturing method. Regarding this approach being time-effective, considerably sensitive and specific, it is expected that it be used in food quality control labs in monitoring systems in future.