The primary part of the body affected by schizophrenia is the brain. People with schizophrenia have brains that look and function differently than people who don’t have schizophrenia. It may be due to the brain-messenger system of neurotransmitters malfunctioning. But schizophrenia affects the body in other ways, too.ecause it is a brain disorder, many of the complications associated with the disease affect the mind or the brain. These complications include depression and self-injury. An extreme effect of schizophrenia on the mind is suicide.