Staphylococcus aureus causes a number of diseases in humans and animals, and is the most common etiological agent of foodborne illnesses. The agent produces staphylococcal enterotoxins (SEs), which are the main cause of food poisoning. The aim of the present study was to characterize the distribution of genes encoding staphylococcal enterotoxins (sea, seb, sec, sed, see, seg, seh, sei, sej, sek, sem, sen, ser and seu) in S. aureus strains isolated from goats slaughtered in four different slaughterhouses in Sichuan, China. The presence of the target 16S rDNA (Staphylococcus genus specific) and nuc gene (S. aureus species specific) was used to determine the isolates to be S. aureus species. Of the 19 S. aureus isolates tested, 18 (95%) were found to be positive for three or more SEs gene (3–7 SEs genes) by polymerase chain reaction (PCR) amplification. The most frequent gene was seu (17/19, 89.5%), followed by seg (14/19, 73.6%), sen (10/19, 52.6%), sei (9/19, 47.3%), and sed (9/19, 47.3%). None of the isolates harbored the genes encoding seb, see, and seh. Among the classical enterotoxigenic strains, the occurrence of sed gene was highest (47.4%) followed by ea (36.8%) and sec (31.6%). The occurrence of the newly identified enterotoxin genes (seg-seu) was higher than that of traditional genes (sea-see). According to the present results, the S. aureus strains isolated from goats seem to be, at least at this stage, of importance as vectors causing staphylococcal food poisoning.