When the Bill & Melinda Gates Foundation said it would pay its next CEO more than its first, it wasn't kidding. While Patricia Stonesifer received a salary of just $1 during her decade-long tenure, the current foundation Chief Executive Jeffrey Raikes receives the largest compensation of any CEO among 49 private foundations surveyed by the...

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When the Bill & Melinda Gates Foundation said it would pay its next CEO more than its first, it wasn’t kidding. While Patricia Stonesifer received a salary of just $1 during her decade-long tenure, the current foundation Chief Executive Jeffrey Raikes receives the largest compensation of any CEO among 49 private foundations surveyed by the Chronicle of Philanthropy. Raikes did not earn as much as the chief investment officers at foundations smaller than the Gates Foundation.

Stonesifer and Raikes were both early Microsoft employees who earned their fortunes building the software company. Stonesifer refused to take a salary at the philanthropy. When Raikes was hired, the Gates Foundation said it did not want to maintain a precedent of not paying its chief executive.

Raikes, who joined the Gates Foundation a year ago, earned $315,403 from September through December 2008, making his annualized salary $990,000, according to the Chronicle.

A Gates Foundation spokesperson confirmed the compensation figures and said the philanthropy’s co-chairs, Bill and Melinda Gates, set the CEO salary “after considering industry standards and what they believe is fair for leading a philanthropic organization of this size and scale.”

Other foundation executives earning top salaries include Joan E. Spero, former president of the Doris Duke Charitable Foundation with compensation of $768,525.

In several cases the chief investment officer earned more than the CEO, such as the $1.6 million compensation of Laurance R. Hoagland Jr. at the William and Flora Hewlett Foundation; $1.4 million paid to John Moehling at the David and Lucile Packard Foundation, or the $1.2 million paid to Susan Manske at the John D. and Catherine T. MacArthur Foundation, the Chronicle reported.

At the Gates Foundation, Tadataka Yamada, president of the global health program, earned $848,390.

The Ford Foundation, which is one-third the size of the Gates Foundation in assets, paid its president, Luis A. Ubinas, $718,084, and vice president, Linda Strumpf, $1,113,590.

Among heads of other non-profits, the highest paid executives include:

James Mongan, chief executive of Partners HealthCare System in Boston, with compensation of $2.7 million in 2008, a 99 percent increase over his 2007 pay.

Glenn Lowry, director of the Museum of Modern Art, in New York, with compensation of $2.1 million in 2008, more than twice his 2007 pay, plus a housing allowance worth $336,000.

The report also shows that the gap in pay between leaders at large non-profits and small charities has grown. Consistently bigger raises over the past several years mean CEOs at larger non-profits now earn almost 10 times as much as those at small ones, according to GuideStar, a research organization that tracks nonprofits.

A gender pay gap persisted among charities, where women held 47 percent of the CEO positions, but received only 35 percent of the total compensation.

Locally, two executives of Seattle non-profits made the Chronicle list for having part of their compensation in the form of a bonus or cash incentive. The Program for Appropriate Technology in Health (PATH) paid President and CEO Christopher Elias $505,129 in total compensation in 2008, including a bonus of $99,561.

At the Casey Family Programs, CEO William C. Bell was paid $567,307, including a bonus of $109,675.

Among the local charities working internationally, World Vision President Richard Stearns received $336,472, and World Vision Senior Vice President Atul Tandon was paid $213,061.

United Way King County CEO Jonathan Fine was paid $242,122, the 19th highest of the 40 United Way leaders around the country. King County is the third largest United Way by income size.