Many parts of pork meat processing are currently not used for human consumption in Switzerland, although they are of great nutritional value. Therefore, data on the occurrence of pathogenic organisms on byproducts is extremely scarce and the prevalence and population structure of
Staphylococcus aureus
on meat processing sidestreams is unknown. Hence, abattoir byproducts of pork origin including ear, forefoot, heart, intestine, liver, rib bone, sternum, bladder, stomach, hind foot and tongue originating from six abattoirs were screened for
S
.
aureus
. The obtained isolates were investigated by
spa
typing and DNA microarray analysis to reveal their genomic profile and population structure. The prevalence of
S
.
aureus
was generally low with a mean of 8%. In total, 40
S
.
aureus
strains were detected and assigned to 12
spa
types (t015, t1491, t1778, t091, t337, t899, t2922, t7439, t1333, t208, t4049, t034) and seven clonal complexes (CC1, CC7, CC9, CC30, CC45, CC49, CC398). Detected enterotoxin genes included
sea
,
seb
,
sec
,
seh
,
sel
and
egc
encoded toxin genes
seg
,
sei
,
sem
,
sen
,
seo
, and
seu
. None of the isolates harbored genes conferring methicillin resistance, but
blaZ/I/R
genes causing penicillin resistance were frequently found. In addition, strains from CC398 exhibited
tetM
and
tetK
, conferring tetracycline resistance. Similarity calculations based on microarray profiles revealed no association of clonal complexes with particular body parts, but revealed a certain correspondence of clonal complex and originating abattoir.