Election workers have until Dec. 5 to complete the recount.
The recount is required under state law because the votes cast for Coleman and Franken differed by less than one-half of 1 percent. Coleman's 215-vote lead heading into the recount translated to 0.008 percent.
The count of nearly 300,000 ballots in Ramsey County - home to the state capital - is likely to take several days.
Before the sorting began, county elections manager Joe Mansky laid out the task and the ground rules: 30,000 ballots to count each day, or one every five seconds for each counter. No one but county election employees or election judges may touch the ballots. No food or drink, no talking.
"What we're going to be looking for today is any ballots where the voter intent is not absolutely clear," Mansky said. "There are very, very few ballots on which we are not absolutely clear."
He also said counting would take place six hours a day. "There is a limited amount of time that you can count or pile ballots without getting a little crazy," Mansky said.
In adjacent Hennepin County, the city of Minneapolis, a Democratic stronghold, was conducting its own recount of all 131 of its precincts.
Minnesota's race looms large in the Washington power struggle.
Depending on another undecided contest in Georgia, the Minnesota outcome could determine whether Democrats attain a 60-seat majority that would enable them to overcome Republican filibusters.
On Tuesday, Sen. Ted Stevens, the longest-serving Republican in Senate history, narrowly lost his re-election bid in Alaska. His defeat by Anchorage Mayor Mark Begich gives Democrats 58 seats, when two independents who align with Democrats are included.
In all, 49 of 107 recount sites - some county, and some city - began their work on Wednesday. A state canvassing board will take up their results and make rulings on disputed ballots beginning Dec. 16. Any litigation could drag a final resolution well into 2009.
Both campaigns were warning their supporters not to read too much into updated recount numbers released at the end of each day.
"It's sort of like watching the stock market these days," said Fritz Knaak, a lawyer representing Coleman in the recount. "It's going to go up, it's going to go down."
Separately Wednesday, Ramsey County Judge Dale Lindman granted Franken's request for the release of information on voters whose absentee ballots were rejected. Franken wants the rosters of disqualified absentee voters in all 87 counties to determine if they were properly rejected.
Lindman's ruling applies only to Ramsey County, the state's second-largest county, but it represents a partial victory for Franken. The state canvassing board hasn't decided whether to allow wrongly rejected absentee ballots into the statewide recount.