On Jul. 1, 1944, the Public Health Service Act (PHS) was codified and established the quarantine authority of the federal government. The act gave the PHS responsibility for preventing the introduction, transmission, and spread of communicable diseases from foreign countries into the United States. The PHS cutter ship was used to transport quarantine inspectors to board ships flying the yellow quarantine flag. The was flown until quarantine and customs personnel inspected and cleared the ship to dock at the port.

When CDC assumed responsibility for Quarantine, it was a large organization with 55 quarantine stations and more than 500 staff members. Quarantine stations were located at every port, international airport, and major border crossing.

Originally part of the Treasury Department, Quarantine and PHS, its parent organization, became part of the Federal Security Agency in 1939. In 1953, PHS and Quarantine joined the Department of Health, Education, and Welfare (HEW). Quarantine was then transferred to the agency now known as the Centers for Disease Control and Prevention (CDC) in 1967. The CDC remained part of HEW until 1980 when the department was reorganized into the Department of Health and Human Services.