In May 1999, Schuldiner experienced pain in his upper neck, which he initially thought was a pinched nerve. He consulted with a chiropractor followed by a massage therapist/acupuncturist who recommended an MRI Exam. He was correct about the pinched nerve; unfortunately, it was being caused by a tumor. On his birthday, May 13, 1999, Schuldiner was diagnosed with pontine glioma, a type of brain cancer that invades the brain stem and immediately underwent radiation therapy.
In October 1999, Schuldiner’s family announced that the tumor had necrotized and that he was on the way to recovery. In January 2000, Schuldiner underwent surgery to remove what remained of his tumor. The operation was a success, however, the Schuldiner family was struggling financially. The total costs of the operations would come to $70,000, a price the Schuldiner family could not afford. Many fundraisers, auctions, and benefit concerts took place to help cover the costs. The money began to come in as the metal community, in total shock, realized that Schuldiner's life was in danger. The metal community and the Schuldiner family showed deep concern because Schuldiner could lose his life due to lack of funds. The doctors who removed his tumor called the original diagnosis of pontine glioma a misdiagnosis.
Schuldiner continued to work on his music, continuing his work with Control Denied. About two years after his original diagnosis, in May 2001, the cancer returned and Schuldiner fell ill again. He was originally denied surgery (which he needed immediately) due to lack of funds. A press release called for support from everyone, including fellow artists. Jane Schuldiner urged all who read the statements about Schuldiner and his illness to go out and get insurance, showing her frustration in the American system. Schuldiner had gotten medical insurance after his first surgery, but the insurer had refused to pay because the tumor existed before he had gotten the insurance. Schuldiner received a chemotherapy drug called vincristine to help with his therapy. Like most drugs used in the treatment of cancer, the side effects were harsh and weakened Chuck greatly. Undaunted, Schuldiner fought on. In late October/early November, Schuldiner became ill with pneumonia. He died on December 13, 2001, at approximately 4 p.m. Eastern Standard Time.