The Nasdaq composite underperformed the major averages as the iShares Nasdaq Biotechnology ETF (IBB) closed down nearly 2 percent. Apple ended about half a percent lower.
Mike Bailey, director of research and chair at FBB Capital Partners, attributed the declines in health care and biotech stocks to negative news around major firms such as Valeant and Celgene.
Celgene reported its smallest revenue growth in five quarters due to slower sales of its two key cancer drugs, Reuters said.
Shares of Facebook ended about 4.6 percent higher after briefly gaining more than 6 percent. The social media giant reported earnings after Wednesday's close that beat on both the top and bottom line.
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The Market Vectors Semiconductor ETF (SMH) closed down 2.59 percent, after four straight days of gains, as Qualcomm fell more than 15 percent after its outlook for the current quarter came in far below expectations. The stock had its worst day since the tech bubble in 2000.
Shares of FireEye plunged 22.87 percent after disappointing earnings, for the stock's worst day since its initial public offering in 2013.
"Today we're just biding our time until our report tomorrow," said John Caruso, senior market strategist at RJO Futures.
"Tomorrow is a pretty pivotal number," he said. "I think it's going to be a lukewarm number. I don't think we're going to see any surprises. It's going to keep everybody guessing."
Ahead of Friday's report on October nonfarm payrolls, weekly jobless claims came in at 276,000, above expectations.
Third-quarter productivity increased at a 1.6 percent annual rate, while labor costs rose 1.4 percent.
U.S. layoffs fell 14 percent in October from the prior month, a 1.3 percent decrease year-over-year, according to Challenger, Gray & Christmas.
Treasury yields held near recent highs, with the 10-year yield at 2.24 percent and the 2-year near 0.85 percent, its highest since 2011.
The U.S. dollar traded flat against major world currencies, with the euro near $1.087 and the yen at 121.74 yen against the greenback.
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Adam Sarhan, CEO of Sarhan Capital, pointed to some initial support for U.S. equities from positive momentum in overseas markets.
China's Shanghai composite closed nearly 2 percent higher Thursday, bringing the index more than 20 percent above its recent low touched on Aug. 26. The composite remains more than 30 percent below its 52-week high hit in June.
The Nikkei closed 1 percent higher.
European stocks pared gains to close mixed, after the Bank of England kept rates unchanged. The German DAX outperformed.
Investors also eyed more comments from Fed policymakers. However, analysts said Fed Chair Janet Yellen's comments and the forthcoming jobs report are most important.
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"If anything way out of the ordinary, sure (markets will react), but otherwise it'll be more the same," Sarhan said.
On Wednesday, Yellen reiterated the possibility of raising rates in December, given supportive data.
New York Fed President William Dudley separately said in a Reuters report that he would "completely agree" with Yellen on a December hike.
In a Thursday speech, Atlanta Fed President Dennis Lockhart said the case for a December hike will continue to strengthen going forward. He also said that labor market slack is "substantially" gone.
Fed Gov. Daniel Tarullo spoke Thursday about bank regulation in prepared remarks, but did not address monetary policy.