On November 21, 1957, Gein was arraigned on one count of first degree murder in Waushara County Court, where he pleaded not guilty by reason of insanity. Gein was diagnosed with schizophrenia and found mentally incompetent, thus unfit for trial. He was sent to the Central State Hospital for the Criminally Insane (now the Dodge Correctional Institution), a maximum-security facility in Waupun, Wisconsin, and later transferred to the Mendota State Hospital in Madison, Wisconsin.

In 1968, doctors determined Gein was "mentally able to confer with counsel and participate in his defense". The trial began on November 7, 1968, and lasted one week. A psychiatrist testified that Gein had told him that he did not know whether the killing of Bernice Worden was intentional or accidental. Gein had told him that while he examined a gun in Worden's store, the gun went off, killing Worden. Gein testified that after trying to load a bullet into the rifle, it discharged. He said he had not aimed the rifle at Worden, and did not remember anything else that happened that morning.

At the request of the defense, Gein's trial was held without a jury, with Judge Robert H. Gollmar presiding. Gein was found guilty by Gollmar on November 14. A second trial dealt with Gein's sanity; after testimony by doctors for the prosecution and defense, Gollmar ruled Gein "not guilty by reason of insanity" and ordered him committed to Central State Hospital for the Criminally Insane. Gein spent the rest of his life in a mental hospital. Judge Gollmar wrote, "Due to prohibitive costs, Gein was tried for only one murder—that of Mrs. Worden. He also admitted to killing Mary Hogan."

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