Charles Tengeri, a retired school teacher, was the first customer to emerge from the Pasadena headquarters of the bank.
He held a check for $171,000 - an amount that he said represented most of his savings.
"I didn't think this could happen," he said. "But I'm glad to get anything out."
Customer Harvey Soldan said he had more than $100,000 in the bank whose assets were seized Friday by federal regulators.
"It's a question of how much we can get and how soon," he said while waiting in line.
Soldan spent Sunday night at a hotel near the bank so he could be at the door more than three hours before it opened at 9 a.m.
Two-hundred people were in line when the bank opened. A security guard at the door was allowing 10 people at a time to enter the branch.
Customers were orderly as the line stretched around the block.
The mortgage lender, which succumbed to the pressures of tighter credit, tumbling home prices and rising foreclosures, is the largest regulated thrift to fail and the second-largest financial institution to close in U.S. history, regulators said.
The Office of Thrift Supervision said it transferred IndyMac's operations to the Federal Deposit Insurance Corporation because it did not think the lender could meet its depositors' demands.
The FDIC insures bank deposits of up to $100,000 per depositor and up to $250,000 for funds in retirement accounts such as an IRA.
Customers with uninsured deposits could begin making appointments to file a claim with the FDIC on Monday. The agency said it would pay unsecured depositors an advance dividend equal to half of the uninsured amount.
As of March 31, IndyMac had total deposits of $19.06 billion. The company operates 33 retail branches, all in Southern California.
Some 10,000 depositors had funds in excess of the insured limit, for a total of $1 billion in potentially uninsured funds, the FDIC has said.
David Barr, an FDIC spokesman, was stationed outside the IndyMac headquarters on Monday. He said people might actually have more money insured than they think.
Customers will be informed about how their accounts are structured and may be eligible to recoup dollar-for-dollar beyond the $100,000 limit, he said.
If deposits aren't fully insured, customers will receive a receivership certificate and told about the process to possibly recoup more of their money.
Barr said it may take several years before the FDIC completely resolves the collapse and addresses customer claims.
"We have to completely unwind the affairs" of the bank, he said. "We may sell a portion to another bank, sell real estate. There may be lawsuits. There are a lot of different aspects to this."
He said the FDIC will waive any early withdrawal penalties for certificates of deposit, with interest paid up to the withdrawal date.
Customer James Sherman said he also had more than $100,000 in the bank.
"This is my life savings here. I feel really horrible," he said.
Sherman said he was hoping to get 50 cents on the dollar above the federally insured limit, with the remainder possibly applied to his mortgage with IndyMac.
"What do you resort to now, putting money back in the mattress?" he asked.
Tengeri said he was hopeful about getting the remainder of his life savings from the bank.
"I'm keeping my fingers crossed," he said. "I have full trust in the U.S. government. It may take a little time but I'm not worried."