Prosecutors said Madigan led a criminal enterprise meant to enhance his political power and financial well-being.
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They also claim he generated income for his allies and associates for nearly a decade.
The attorney for co-defendant Michael McClain also pleaded not guilty on all counts.
RELATED: No perp walk for ex-Illinois House Speaker Mike Madigan
Tuesday's arraignment was over the phone.
Madigan was not present on the call.
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The case is next due in court Nov. 17.
AT&T Illinois recently agreed to pay a $23 million fine for trying to illegally sway Madigan by steering $22,500 to a Madigan ally as key legislation moved through Springfield.
Sun-Times Media contributed to this report.