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Einhorn's Athenahealth short is nothing new

Source: Athenahealth | Facebook

Hedge fund manager David Einhorn caused Athenahealth's stock price to drop about 13 percent Tuesday when he called the company's valuation a "bubble" in a scathing presentation at the Sohn Investment Conference in New York City Monday evening.

Read MoreDavid Einhorn tells investors to short Athenahealth

Despite all the hoopla, Einhorn's Greenlight Capital is hardly the first to bet against the fast growing health-care service and software company. The percent of Athenahealth shares on loan—a common measure of how much investors are shorting—is 17.7 percent of outstanding stock, according to data tracker Markit. That's down from about 32 percent in March 2010, 35 percent in March 2012 and 22 percent in October 2013.

Shorting of the company decreased substantially this spring after the company's stock fell from record highs, suggesting short sellers were taking profits, or closing positions that made money after their short shares fell in value. But bets against Athenahealth have surged in the last four weeks, according to Markit.

"It's been a tough short to call—share prices have been volatile. But it's certainly been the target of short sellers before," said Simon Colvin, a research analyst with Markit.

Read MoreThese are hottest stock picks at Sohn conference

Holly Spring, Athenahealth's director of communications, issued this statement Tuesday in response Einhorn's comments.

For more than a decade Athenahealth has been one of the nation's fastest growing health care IT companies because of its unique business model and ability to drive unmatched value for health care providers. Health care is desperate for disruptive technologies and Athenahealth is one of the few bright spots of innovation. We remain fully confident in our business model and growth projections, and are as focused as ever on delivering on our mission to be caregivers' most trusted service.

Read MoreEinhorn: Tech bubble brewing, shorting momentums

—By CNBC's Lawrence Delevingne.

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