A report filed Friday by library security staff to the Harvard University Police Department said a bottle assumed to have contained the urine was found near the vandalized books, the Harvard Crimson newspaper reported.
Due to the subject matter of the books, HUPD is investigating the incident as a hate crime, the Crimson said.
"The HUPD has zero tolerance for any bias-related incidents or crimes," police spokesman Steven G. Catalano said.
The books will be discarded due to the severity of the damage, library staff said.
"Once the urine is poured, they can't really fix [the books]," Harvard College Library spokeswoman Beth S. Brainard said.
Marco Chan, co-chairman of the Harvard College Queer Students and Allies, called the incident "extremely frustrating" and "disconcerting."
"I am very outraged. It is hard to conceive this as a coincidence when there are 40 books on the same subject," Chan said.