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A total of 100 Jordanian clinical Staphylococcus aureus isolates was analysed for the presence of the enterotoxin genes sea, seb, sec, sed and see using multiplex PCR. Twenty-three isolates (23 %) were potentially enterotoxigenic. The prevalence of sea, sec and sea plus sec among the total clinical isolates was 15, 4 and 4 %, respectively. None of the isolates harboured sed, seb or see genes. S. aureus isolates were subjected to DNA fingerprinting by randomly amplified polymorphic DNA (RAPD) analysis to test whether isolates harbouring the toxin genes were genetically clustered. A total of 13 genotypes was identified at a 47 % similarity level. Genotypes I and V accounted for the largest number of enterotoxigenic isolates (19 %). This study has demonstrated the genetic diversity of Jordanian clinical S. aureus isolates and shown that the presence of the toxin genes is not genotype specific.