Orchestra officials said Sunday that the Italian conductor is suffering from "extreme gastric distress" and must fly back to Milan to consult with doctors.
Muti missed Saturday's annual Symphony Ball, and the orchestra performed the sold-out show without a fill-in conductor.
The 69-year-old Muti was scheduled to conduct fall concerts, return for a winter series in February and then conduct two spring sequences.
A spokeswoman says the orchestra hopes Muti can return for the rest of his residency.
Muti first conducted the orchestra more than three decades ago, and his return to Chicago had been highly anticipated.
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