Some of America's largest university endowments unveiled eye-popping annual gains in the past week. Duke University reported a 56% return for the fiscal year ended June 30. Washington University in St. Louis generated a 65% gain.

These top-performing endowments can thank alternative assets—in particular, venture capital—for the banner year, which is said to be the best since 1986. But that short-term success could prove to be a double-edged sword.