Moody's reports the facts:
The top 10 private names are familiar: Harvard University ($42.8 billion in cash and investments in fiscal 2014), Stanford University ($31.6 billion), Yale University ($25.4 billion), Princeton University ($21.3 billion), Massachusetts Institute of Technology ($15.2 billion), University of Pennsylvania ($11.9 billion), Duke University ($11.4 billion), Northwestern University ($10.4 billion), Columbia University ($9.9 billion) and University of Notre Dame ($9.5 billion).
Lists like this give a slightly misleading impression because they don't mention the size of the student body and, most importantly, the presence or absence of professional schools (which are expensive, especially Medicine). The wealthiest university on this list, in reality, is Princeton, which has neither Law, nor Medical, nor Business Schools. MIT doesn't have Law or Medicine. Notre Dame doesn't have Medicine. All the others have all three.
The wealthiest "public" is the University of Texas system, with over 36 billion (including law, medical, and business schools--in some cases more than one!). It serves somewhere in the vicinity of 160,000 students. Princeton, with its mere 21.3 billion, serves about 8,000 students.
I take it these figures also don't include real estate. Columbia's endowment, given its location, is rather non-competitive with Harvard, Stanford, Princeton et al., but Columbia's real estate holdings (including housing for faculty) are huge. I don't know of a source for those figures.
UPDATE: Roger Albin, a professor of medicine at Michigan, notes that, "Academic medical centers generally (and have to) pay for themselves via clinical income," rather than through endowments. He also offers some interesting detail I was completely unaware of regarding Harvard:
The situation is somewhat different for institutions that are involved in academic medical centers but don't own their hospital systems. The most important case is Harvard, which does not own its teaching hospitals. These are financially separate systems which employ Harvard appointed faculty. The Partners system (Massachusetts General Hospital and Brigham & Womens) and Boston Children's, to name the most important, actually pay for most of the faculty at the Harvard Medical School, and have their own separate endowments. The enormous Harvard endowment covers fewer faculty than you might think, one of the reasons they can afford to pay relatively high salaries in many fields. There are also some negative examples in this category. The very fine Baylor College of Medicine used to staff the Methodist Hospital system in Houston. Baylor and Methodist had a falling out over finances and split, leaving Baylor in a very challenging financial situation.
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