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Auburn (4-0) trailed 7-0 early, but rallied with an impressive offensive showing, gaining 487 yards.
Todd's aerial show included touchdowns of 46 yards and 65 yards to Terrell Zachery in the second quarter. Zachery had five catches for 122 yards.
Onterio McCalebb rushed eight times for 86 yards for Auburn.
Kelly Page passed for 101 yards and one touchdown and ran for another to lead the Cardinals (0-4).
Auburn continued its impressive early season offensive showing. The Tigers have scored 181 points so far this season, the most ever for Auburn in its first four games.
Kickoff was delayed for 30 minutes because of heavy rain and lightning. It was the second week in a row that storms had delayed the start of an Auburn game. Last week's game against West Virginia was delayed for more than an hour by rain and lightning.
Todd's five touchdown passes tied the Auburn record set by Daniel Cobb in an overtime game against Louisiana Tech in 2001.
In addition to the two long scoring passes to Zachery, Todd had scoring passes of 26 yards to Darvin Adams, 36 yards to Mario Fannin and 6 yards to Tommy Trott.
Ball State refused to give up, scoring 20 points in the second half, mostly against Auburn substitutes.
Auburn backup quarterback Neil Caudle got into the game in the second half and scored on 52-yard run up the middle.
Ball State of the Midwest Athletic Conference put an early scare into the heavily favored Tigers of the Southeastern Conference, jumping out to a 7-0 lead less than three minutes into the game. The score came after Auburn's Anthony Gulley fumbled a Ball State punt and Kyle Hoke recovered at the Auburn 18. The Cardinals scored four plays later on a 2-yard run by Miquale Lewis.
Auburn got it's offense going late in the first quarter after Josh Bynes recovered a fumble by Cardinals' quarterback Kelly Page. The Tigers then drove 29 yards in five plays, scoring on a 6-yard pass over the middle from Todd to Tommy Trott. It was Trott's third career touchdown catch and first since 2006.
Auburn quickly turned the game into a blowout after that, scoring 23 points in the first 7 minutes of the second quarter. The offensive burst included the two touchdown bombs to Zachery and an impressive 65-yard run by McCalebb to the Auburn one-yard-line. McCalebb scored on a 1-yard run a play later.
Ball State's only other score in the first half came on Ian McGarvey's 33-yard field goal.
Auburn's Wes Byrum kicked a 33-yard field goal at the end of the first half. It was his sixth field goal in six attempts this season. The six consecutive field goals is a career best for Byrum.
