Warren Buffett's Berkshire Hathaway sharply reduced its holdings of Kraft Foods and Mondelez during the second quarter.

The company's quarterly filing with the SEC shows Berkshire held just 192,666 shares of Kraft Foods as of June 30. That's a drop of 88 percent from its reported holdings as of March 31.

Mondelez was cut by 91.8 percent to 578,000 shares.

The two companies were created by a split up of Kraft Foods Inc. in October, 2012.

(Read more: Berkshire's Heinz squeezes out 600 employees)

Berkshire increased its General Motors holdings by 60 percent to 40 million shares. That stake is worth $1.4 billion now.

Berkshire added shares of U.S. Bancorp. Its holdings jumped 27.4 percent higher to 78,277,301 shares, now worth almost $2.9 billion.

It also bought more Bank of New York Mellon, raising that stake by 30.1 percent to 24,644,029 shares, currently valued at $747 million.

Berkshire's position in Moody's dropped by 12.3 percent, as previously disclosed, while National Oilwell Varco increased by 18.6 percent.

Berkshire disposed of its entire 1.7 million share Gannett stake in the quarter, currently $42.6 million.

Berkshire's stake in Chicago Bridge & Iron soared 46.7 percent to 9,550,755 shares. They're currently valued at almost $577 million.

It also tripled its shares of Verisign to 10,897,420, with a market value of $534 million.

Berkshire is reporting a new stake in Dish Network of 547,312 shares. That's worth about $24 million at the stock's Wednesday close.

Suncor Energy has also been added to Berkshire's portfolio with 17,769,457 shares. They're now worth $586 million. The Canadian energy company has been working with the Alberta oil sands.

The smaller the size of the position, the more likely it's the work of one of Berkshire's portfolio managers, not Buffett himself. For Suncor, however, it's worth noting that in 2008 he and Bill Gates made a "quiet" visit to the area.

Buffett has said that the portfolio managers, Todd Combs and Ted Weschler, don't need or get his approval before buying or selling shares and their positions in any given stock are generally smaller than $1 billion.

(Read more: Berkshire Hathaway's 15 Biggest Stock Holdings)

There is a line in the filing that "confidential information" was omitted and filed separately with the SEC.

That's an indication Berkshire is accumulating shares in a stock but doesn't want copycats to drive up its price.

Contrary to other media reports, Berkshire made no changes in its holdings of American Express and Coca-Cola. There was a small 1.1 percent increase for Wells Fargo.

(Read more: Warren Buffett sees 'betrayal' as hospital drains big endowment)

In the first quarter of this year, Berkshire eliminated its holdings of two stocks: Archer Daniels Midland and General Dynamics,

Berkshire also added a 6.5 million share stake in Chicago Bridge & Iron.