Princeton University’s endowment outperformed Yale’s in the fiscal year ending in June 2008, posting a 5.6 percent return that grew the fund to $16.4 billion, Princeton said this week.

But Princeton’s endowment gains have receded an undisclosed amount since June, a sign of current economic turmoil and a warning that the coming year could bring disappointing returns or even losses.

The announcement of only slight growth across the Big Three follows several consecutive years of double-digit returns, with Yale’s investments in the lead. Until last year, Yale’s average annual return for the past decade was 17.8 percent, more than two percentage points higher than any other large university fund in the country. In 2006 Yale’s endowment returned a nation-leading 28 percent.

Last year, however, the fund gained 4.5 percent, rising to $22.9 billion. That return placed it behind both Princeton and Harvard, which posted a 8.6 percent return on its $36.9 billion endowment, the largest of any university.

All three funds still beat the market last fiscal year. The S&P 500 Index posted a 13.1 percent loss in the year ending June 30, for instance, and the median return among 165 large institutional funds tracked by the Trust Universe Comparison Service was a 4.4 percent decline.

Yale’s success over the last several years has been partly attributed to alternative investments such as venture capital, oil, gas and timber. Stakes in these assets have helped the funds at Harvard, Yale and Princeton continue to gain while world financial markets plummeted, reports from all three schools have said.