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First there was the "flash crash." Now there's the "flash freeze."

The nation's second-largest stock exchange, the Nasdaq, stopped trading for three hours Thursday after what it called a problem affecting quote dissemination. When trading resumed, however, the shutdown left few visible scars.

The glitch threw trading into turmoil for dozens of publicly traded companies, including high-profile firms such as Apple, Microsoft and Facebook. All traffic for the more than 3,000 shares traded on Nasdaq stopped at 12:14 p.m., the exchange said on its website.

In a statement, Nasdaq officials said that the problem lasted just half an hour, and that the delay took much longer because they wanted to ensure an "orderly re-opening of trading."

The market fully reopened at 3:25 p.m., about half an hour before the closing bell, with the index about 33 points higher. During that brief time, it rose another 5 points to close just over 1 percent higher at 3,638.71.

Once trading got the OK to start again, traders were given a five-minute grace period in which to submit quotes, trade imbalances and conduct other business matters.

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There was a spike in volume, particularly from computerized trading programs that aren't set up to handle a lengthy shutdown from a major global exchange.

(Read more: Stocks close higher, even after 3-hour Nasdaq shutdown)

The shutdown brought vehement criticism from across Wall Street.



"The negative impact is going to be felt tomorrow," said Todd Schoenberger, managing director at LandColt Capital. "Obviously this technology is failing. The lack of transparency—we haven't heard from the Nasdaq, we haven't heard from Washington—it creates chaos and uncertainty.

"You're going to have investors thinking, 'This is the Wild, Wild West and I don't want to be in this market.'"

Dennis Gartman, editor and publisher of The Gartman Letter, said: "This is such an embarrassment to the entire financial community. To have the Nasdaq go down as it has; to be down three hours—it's one thing to be down for five minutes—to be down for three hours is absolutely inexcusable."

(Read more: 'Knight-mare': Trading Glitches May Just Get Worse)



But an investor with regulatory experience said there wasn't much damage because of the timing: a Thursday afternoon in August.

"It will affect people who really need liquidity and were planning to get it from Nasdaq stocks," the investor said. "These things happen nowadays, markets break down, it's an assumed risk of trading that the market you need to trade in could break down."

The Nasdaq famously shut down for 82 minutes in December of 1987 when a squirrel caused a power failure in Trumbull, Conn., where Nasdaq's main computer center was located.

The delay Thursday was yet another black eye for a market that has suffered through flash crashes, embarrassing glitches in initial public offerings and a general perception of being an uneven playground.

The "flash freeze" echoed the so-called "flash crash" in 2010, that erased several hundred points from the bellwether Dow Jones industrial average in minutes.



CNBC's Jeff Cox, NBC's Steve James and Reuters contributed to this report.