The unbeaten Tigers (8-0) vaulted from fourth to the top spot Sunday, putting the Southeastern Conference in line for a fifth straight appearance in the national title game.
Oregon (7-0) remained second, which works just fine for the Ducks because if they win out they'll likely play in the BCS title game in Glendale, Ariz., in January.
Boise State (6-0) was still stuck in third place. The Broncos were off last week while Auburn beat LSU 24-17 and Oregon pounded Pac-10 rival UCLA 60-13.
Missouri's jump to sixth comes a day after the Tigers knocked off previous BCS No. 1 Oklahoma. The Sooners fell all the way to ninth in the second installment of this season's standings after their 36-27 Saturday night road loss.
Auburn was tops in the computer rankings and third in each of the USA Today coaches' and Harris polls. The polls count for two-thirds of a BCS average and a compilation of six computer ratings accounts for the rest.
"I can only control how we proceed in this building," coach Gene Chizik said a few hours before the standings were released. "We just had a team meeting and we talked about being very grounded and understanding that every week is another new week and another opportunity."
An SEC team has won the past four national championships, with Florida taking two and Alabama and LSU winning one each.
Oregon's computer rating was still lagging behind most of the top teams at eighth, but the Ducks were a solid No. 1 in each of the polls.
Boise State was No. 2 in the polls and the computers had the Broncos sixth.
Boise State from the Western Athletic Conference and TCU from the Mountain West are both trying to become the first teams from conferences without automatic bids to play in the BCS Championship Game. To have any chance, they'll have to go undefeated and have Auburn and Oregon lose.
Even then, the Broncos and Horned Frogs could be passed by Michigan State and Missouri if they stay unbeaten, or maybe even by Alabama, which has lost a game but stands seventh in the BCS standings.
Oregon and Auburn both play on the road this week. The Tigers play at Mississippi and Oregon is at Southern California.
Boise State plays Tuesday night at home against Louisiana Tech.
Information from The Associated Press was used in this report.