The U.S. District Court for the Southern District of California, as we know it today, is relatively new in the organization of U.S. Courts.

San Diego was part of the old Southern District established by Act of Congress on August 5, 1886, with headquarters in Los Angeles. On March 1, 1929, the Southern District was divided into three divisions. San Diego and Imperial Counties were designated the Southern Division of the Southern District of California, holding semi-annual sessions in July and January. Los Angeles and surrounding counties became the Central Division and Fresno and surrounding counties became the Northern Division.

Very little information is available relative to the conduct of federal judicial business in San Diego between the years 1886 and 1929. If court sessions were held, they were probably presided over by one of the judges from the Central Division, as San Diego did not receive a resident federal judge until 1949. On March 19, 1946, the Honorable Jacob Weinberger entered on duty as a judge of the Southern District of California assigned to Los Angeles, and on November 1, 1949, Judge Weinberger was assigned as the first resident federal judge in San Diego.

On September 19, 1966, pursuant to Public Law 89-372, March 18, 1966, the Southern District of California established in 1886 ceased to exist. Four new judicial districts in the State of California were created. San Diego and Imperial Counties became the new Southern District of California with headquarters in San Diego.

Currently, the Southern District of California has 13 active district judges, five senior district judges, nine full time magistrate judges in San Diego. A tenth full time magistrate judge sits in El Centro. While the district courts receive both civil and criminal filings, the Southern District of California is well known for its criminal caseload. Because of its proximity to the border, the Southern District of California has the highest criminal caseload per active judge in the country. The majority of the criminal cases filed in this district involve drug trafficking and illegal immigration.