This study aimed to evaluate the presence of enterotoxigenic S. aureus in the endogenous starter and in Artisan Minas cheeses from the Serra da Canastra. Sixteen samples of endogenous starters and cheese were collected during the rainy and dry seasons. The isolation and enumeration of S. aureus were performed using the PetrifilmTM-Rapid S. aureus Plate Count method. The presence of enterotoxin in the cheese samples was analyzed by the Optimal Sensitivity Plate (OSP) method and the ELFA-VIDAS®-Staph enterotoxin-II assay. S. aureus strains were tested for their ability to produce enterotoxins using the Optimal Sensitivity Plate (OSP) method and the polymerase chain reaction (PCR) assay for the classical enterotoxin genes. The Optimal Sensitivity Plate (OSP) method data showed that staphylococcal enterotoxin A (SEA) was detected in 75% of the cheese samples, but no toxin was detected with the ELFA-VIDAS method. It was found that 12.5% of the isolated strains produced staphylococcal enterotoxin A (SEA) and staphylococcal enterotoxin C (SEC). When using the the polymerase chain reaction (PCR) assay, only one isolate was found to harbor an enterotoxin gene, contrary our expectations. However, discrepancies between the immunological and molecular assays are not uncommon. Despite the fact that most isolates did not produce classical enterotoxins, high S. aureus counts in the cheese samples causes concern since there is a risk of the presence of non-classical enterotoxins.