David Einhorn's Greenlight Capital has cut its stakes in high-flying technology companies Apple, Twitter and Micron, according to new SEC filings covering positions through the end of the second quarter.

The billionaire's hedge fund reduced its stake in Apple by 486,000 shares, or 77 percent, according to a required 13F filing with the Securities and Exchange Commission on Tuesday. The fund also decreased its position in Twitter by 901,400 shares, or 36 percent.

Greenlight also cut its stake in Micron by 3.1 million shares, or 92 percent.

Shares of all three technology names have soundly outperformed the market this year. Year to date through Monday Apple rose 23.4 percent, Twitter increased 36.6 percent and Micron rallied 24.9 percent, respectively, versus the S&P 500's 5.6 percent gain.

Despite those gains, Greenlight is having a difficult year. Last month, Einhorn admitted his fund has dramatically underperformed his expectations.

"Over the past three years, our results have been far worse than we could have imagined, and it's been a bull market to boot," Einhorn said in a letter to investors. "Right now the market is telling us we are wrong, wrong, wrong about nearly everything."

The letter revealed Greenlight Capital lost 5.4 percent in the second quarter, bringing its year to date loss to 18.3 percent through the end of June. The S&P 500 gained 2.6 percent this year as of the end of June.

— CNBC's Hugh Son contributed reporting.