The 1999 Southern Illinois Salukis football team represented Southern Illinois University as a member of the Gateway Football Conference during the 1999 NCAA Division I-AA football season. They were led by third-year head coach Jan Quarless and played their home games at McAndrew Stadium in Carbondale, Illinois. The Salukis finished the season with a 5–6 record overall and a 1–5 record in conference play.
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