Background: Methicillin-resistant Staphylococcus aureus (MRSA) is a multidrug-resistant microorganism and the predominant nosocomial pathogen all over the world. The potential benefits of probiotic lactobacilli against pathogenic bacteria have been shown in many studies. Objectives: This study aimed to investigate the effect of cell-free culture supernatant (CFS) of probiotic Lactobacillus spp, including Lactobacillus reuteri, L. plantarum, and L. fermentum, on virulence factor gene expression of MRSA. Methods: Lactobacilli were cultured in MRS and the cells were harvested by centrifuging at 10,000 × g for 10 min at 4°C. The pellet was discarded and 1/2 and 1/4 CFS concentrations from Lactobacillus spp were added to the medium (MHB) containing 10 7 CFU/mL of the MRSA strain. A quantitative polymerase chain reaction (qPCR) was performed to measure the expression of virulence factors at the transcriptional level. Results: The results showed that lactobacilli CFS had no obvious inhibitory effects on the growth of S. aureus. The qPCR assay showed that the expression levels of sea, sae, agr A, tst, spa, and spi genes reduced at different levels, depending on the concentration of CFS and the species of lactobacilli so that the maximum significant down-regulation rate was observed in the sea and tst genes (up to 23.5 folds in the presence of 1/2 concentration of L. reuteri CFS after 12 h incubation). Conclusions: Cell-free culture supernatants of probiotic bacteria can down-regulate the virulence genes. Consequently, toxins and enzymes are less produced by S. aureus as a food-borne pathogen. Therefore, the presence of CFS in the food probably reduces diarrhea and vomiting caused by S. aureus.