The family was given the choice of either waiting up to three weeks for Jackson's brain to be returned to them or go ahead and bury him without it - which they have decided to do.
Los Angeles Coroner's spokesman Craig Harvey said that neuropathology tests are going to be conducted to see if it holds any clues to the exact cause of his death.
However, the examination cannot start until at least two weeks after the death when the brain has hardened sufficiently to slice it open.
Sources at the coroner's office revealed that his brain was removed before his body was released to relatives the next day.
Jackson's death is believed to have stemmed from a suspected overdose of painkillers.
Jackson's brain will be tested by a forensic neuropathologist for past drug use and whether he has suffered overdoses in the past.
The brain can also show any past abuse of alcohol or if the singer had suffered from any one of a number of diseases.
According to the source, removing the brain is the "only way to carry out the tests".
"The tissue has to be examined. I can't tell you how long that is going to take," the Mirror quoted the source as saying.