Apple briefly fell more than 3 percent to hit a fresh 52-week intraday low to weigh on the Nasdaq composite, which closed nearly half a percent lower after dipping 1 percent intraday.
Read MoreApple just sent up another red flag for stocks
"Anytime you have weakness in a market leader you have to be careful," said Anthony Valeri, investment strategist at LPL Financial.
Apple and Gilead Sciences had the greatest negative impact on the Nasdaq 100, while Microsoft and Amazon.com contributed the most to gains. The iShares Nasdaq Biotechnology ETF (IBB) closed 1.7 percent lower.
"Beta is for sale. Apple is weak, not much technical support," said Ilya Feygin, managing director and senior strategist at WallachBeth Capital.
"I think it's a slightly negative combination of weaker growth and no change in the Fed," he said.
Read MoreAlphabet solidifying No. 1 spot
In economic news, weekly jobless claims rose to 294,000. Import prices rose 0.3 percent in April, while export prices rose 0.5 percent.
Treasury yields held higher, with the 2-year yield near 0.75 percent and the 10-year yield around 1.75 percent. The Treasury also held a $15 billion sale of 30-year bonds that was met with weak demand.
"Tomorrow, retail sales are either going to confirm things really are weak or it will show the employment number and the GDP number was temporary weakness," said Bryce Doty, senior fixed income manager with Sit Investment Associates. "Maybe it's looking more forward to tomorrow morning."
The U.S. dollar index was roughly 0.4 percent higher, with the euro last near $1.137 and the yen near 109.1 yen against the greenback.
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On Wednesday, stocks closed lower despite gains in oil prices as disappointing retail earnings renewed concerns about consumer spending levels ahead of April retail sales, due Friday. The SPDR S&P Retail ETF (XRT) fell 4.4 percent for its worst day since August 2011.
The ETF closed 0.26 percent lower Thursday.
"When you're kind of directionless one little thing can move the market," said Maris Ogg, president, Tower Bridge Advisors.
"I think the market is really hamstrung by its valuation. You're just swinging around one direction to another and it's not making a difference," she said.
Boston Fed President Eric Rosengren, a voting member, said in a speech the markets are underestimating the pace of potential rate hikes by the central bank. In another speech, Cleveland Fed President Loretta Mester said inflation weakness has been driven by transitory oil weakness and a strengthening dollar.
Kansas City Fed President Esther George, another voting member, said in a Reuters report the Fed is keeping interest rates too low and risks encouraging companies to take on excessive amounts of debt.
European stocks closed lower, with the German DAX falling more than 1 percent.
Asian stocks ended mixed, with the Nikkei 225 0.4 percent higher and the Shanghai composite a touch lower. The Hang Seng closed 0.7 percent lower.
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The Dow Jones industrial average closed up 9.38 points, or 0.05 percent, at 17,720.50, with Nike the top advancer and Apple leading decliners.
The S&P 500 closed down 0.35 points, or 0.02 percent, at 2,064.11, with telecommunications leading seven sectors higher and health care the greatest laggard.
The Nasdaq composite closed down 23.35 points, or 0.49 percent, at 4,737.33.
The CBOE Volatility Index (VIX), widely considered the best gauge of fear in the market, traded near 14.4.
Decliners were a step ahead of advancers on the New York Stock Exchange, with an exchange volume of 931 million and a composite volume of 3.7 billion.
Gold futures for June delivery settled down $4.30 at $1,271.20 an ounce.
On tap this week:
Earnings: Nordstrom, Nvidia, Symantec, Shake Shack
Earnings: Honda Motor, Brookfield Asset Mgmt., JC Penney
8:30 a.m. Retail sales
8:30 a.m. PPI
10 a.m. Consumer sentiment
10 a.m. Business inventories
6:25 p.m. San Francisco Fed's Williams
*Planner subject to change.
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