Given the potential risks surrounding the procedure, cerebral biopsy is indicated only if other diagnostic approaches (e.g. magnetic resonance imaging) have been insufficient in showing the cause of symptoms, and if it is felt that the benefits of histological diagnosis will influence the treatment plan.

The procedure can also be valuable in people who are immunocompromised and who have evidence of brain lesions that could be caused by opportunistic infections.

In other groups, particularly those with unexplained neurological disease, a diagnosis is reached by performing a biopsy in half the cases where it is done, and it has helpful practical effect in 30% of people.

If primary angiitis of the central nervous system (PACNS) is suspected, brain biopsy is most likely to positively influence the treatment plan.

A small hole is drilled into the skull, and a needle is inserted into the brain tissue guided by computer-assisted imaging techniques (CT or MRI scans).