One of the missing brains is believed to have belonged to clock tower sniper Charles Whitman.
"We think somebody may have taken the brains, but we don't know at all for sure," psychology Professor Tim Schallert, co-curator of the collection, told the Austin American-Statesman.
His co-curator, psychology Professor Lawrence Cormack, said, "It's entirely possible word got around among undergraduates and people started swiping them for living rooms or Halloween pranks."
The Austin State Hospital had transferred the brains to the university about 28 years ago under a "temporary possession" agreement.
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"They are no longer in the basement," Cormack said.
The university said in a statement that it will investigate "the circumstances surrounding this collection since it came here nearly 30 years ago" and that it's "committed to treating the brain specimens with respect."
It says the remaining brain specimens on campus are used "as a teaching tool and carefully curated by faculty."
The university's agreement with the hospital required the school to remove any data that might identify the person from whom the brain came.
"It would make sense it would be in this group. We can't find that brain," he said.
Whitman's 1966 rampage at the University of Texas killed 16 people, including his mother and wife.
Eleven of the victims were fatally shot by Whitman who had barricaded himself on the observation deck of the University of Texas Tower before he was killed by police.
The 100 remaining brains at the school have been moved to the Norman Hackerman Building, where they are being scanned with high-resolution resonance imaging equipment, Cormack said.