He and his staff practiced experimental surgical bacteriology on patients, including the routine removal of some or all of patients' teeth, their tonsils, and frequently spleens, colons, ovaries, and other organs. These practices continued long after careful statistical reviews falsified Cotton's claims of extraordinarily high cure rates, and demonstrated very high mortality and morbidity as a result of these aggressive and dangerous measures. As well as the medical horrors he forced upon the patient/victims, Cotton still instituted many progressive ideas after becoming medical director of the Trenton State Hospital at the age of 30. These included abolishing mechanical restraints and implementing meetings of daily staff to thrash out patient care.