The aim of this study was to characterize enterotoxigenic Staphylococcus aureus recovered from raw cow milk from two geographical regions of Poland using pulsed-field gel electrophoresis (PFGE) and multilocus sequencetyping (MLST). Among 610 samples tested, 229 (37.5%) were positive for S. aureus and 30 (13.1%) of them possessed at least one gene encoding enterotoxins. The sec marker was the most commonly identified (12; 40.0% isolates), followed by the sed (9; 30.0%), sea (6; 20.0%), and seb (1; 3.3%) genes. Some S. aureus possessed a combination of the sea and sec or sea and seb toxin markers. Only two (6.7%) of the enterotoxin gene-positive isolates were not able to produce enterotoxins in vitro. Genotypic analysis with the PFGE method of a total of 50 toxigenic S. aureus isolates from the present and previous studies identified 16 clonal groups. Furthermore, MLST revealed the presence of 15 sequence types with the most common being ST45 and ST1. The results of this study indicate that raw cow milk may be a source of S. aureus with classical enterotoxin genes, which may pose a potential threat for the consumers’ safety.