When the Japanese attacked Pearl Harbor the following year, Clark was named by Attorney General Francis Biddle as the Civilian Coordinator of the Alien Enemy Control Program.

[10] Clark had been reassigned to Washington in May 1942 and was not directly involved with the internment of Japanese Americans in concentration camps,[11] although he later acknowledged that the government's relocation program was a mistake.

[14] One of President Truman's first changes in the cabinet that he inherited from Franklin Roosevelt was his appointment of Tom Clark as attorney general in 1945, a switch made in part because of the close personal and professional relationship shared by the two men.

[16] As attorney general, Clark initially continued to focus a good deal of the department's energy on prosecuting war fraud crimes, as well as aggressively taking on potential antitrust violations.

Clark and the White House also challenged John Lewis, the head of the United Mine Workers union, who was threatening a national strike.

The most important of the briefs he filed was in Shelley v. Kraemer (1948), helping to convince the Court to strike down racial covenants in housing contracts restricting the sale of property to blacks.

[26] After playing an active role in reelecting Truman in 1948, Clark made clear to the White House that he was planning to return to Texas and the practice of law.

[28] Numerous attacks from across the political spectrum were leveled at the nomination, including charges of "cronyism," a lack of judicial experience, and objections based in part on his work at the center of Truman's anti-communist agenda and, specifically, the Attorney General's List of Subversive Organizations.

For the remainder of his tenure on the Court, Clark served alongside Chief Justice Earl Warren, producing a mix of opinions that makes it difficult to characterize him as either conservative or liberal.

Several rulings by the Vinson Court, most notably Sweatt v. Painter and McLaurin v. Oklahoma State Regents (1950), which held that black graduate students must be allowed into "white" state universities and law schools because the separate black school could not provide an education of equal quality, helped lay the groundwork for holdings including Brown v. Board of Education (1954).

Clark played a critical behind-the-scenes role in Sweatt and McLaurin that shaped the discussion and provided a workable solution on this issue, helping to "move the Court from considering equality only as a measurable mathematical construct … to what would become known as intangibles.

"[37] Clark's role as one of two southern justices gave him additional impact in those cases, such as Hernandez v. Texas (1954), in which the Court ruled that excluding persons of Mexican ancestry from juries violated the Constitution.

He also authored several important decisions on race in the 1960s during the height of the Civil Rights era, including Anderson v. Martin (1964), which held unconstitutional a Louisiana statute because it required the races of those running for office to be printed on a ballot, Burton v. Wilmington Parking Authority, which upheld the concept of state action to find that a private restaurant violated the 14th Amendment's Equal Protection Clause, and Heart of Atlanta Motel v. United States and Katzenbach v. McClung, which upheld the public accommodations provision of the 1964 Civil Rights Act.

Garner v. Board of Public Works (1951) was a 5–4 decision he authored that upheld the right of a city to require its employees to file affidavits that they were not, nor had ever been, members of the Communist Party and to take loyalty oaths to that effect.

But Clark also demonstrated a willingness to strike down such laws when they were excessive or overly broad in their application, specifically when they involved the question of whether an individual knew of the organization with which they were allegedly affiliated.

Among the most memorable was his solo dissent in Jencks v. United States, in which he labeled the Court's action a "big mistake," and suggested that allowing an individual charged with falsely swearing that he was not a member of the Communist Party to see reports made by two FBI witnesses against him, "afforded him a Roman holiday for rummaging through confidential information as well as vital national secrets."

Clark's dissent sparked congressional legislation overriding the Court's decision and placing limits on the kinds of documents criminal defendants can request.

[39] Even as he would demonstrate more progressive views in other areas of the law, Clark continued to exhibit his belief in the government's power to prevent people with certain associations from holding certain jobs.

Thus, as late as 1967, he dissented in Keyishian v. Board of Regents, in which the Court struck down as unconstitutionally vague a law preventing a state university from hiring "subversives."

Six years later, however, he joined with his more liberal brethren in the landmark decision Gideon v. Wainwright (1963) upholding the right to a fair trial and due process under the Sixth Amendment and holding that an individual defendant must have an attorney appointed for him if he cannot afford one.

Clark's law enforcement background led him to support this approach because he believed that having a district attorney and a federal prosecutor operating under the same system would ensure that police would be more disciplined and that it would lower the risk of evidence being disallowed.

[40] Clark demonstrated this progressive understanding right up through his final day on the bench, writing Berger v. New York (1967), an important Fourth Amendment decision in which the Court held unconstitutional a state statute allowing electronic eavesdropping.

Clark also wrote the decision for the Warren Court in a major religion case involving the First Amendment's Establishment Clause and reinforcing the principle of separation of church and state.

"[43] During his career, Clark balanced an underlying judicial restraint with a more expansive, yet principled reading of the Constitution and he demonstrated a rare capacity for change and growth.

"[44] Ultimately, Clark came to more fully understand, as he wrote in 1970, that the Constitution "is a living instrument which also must be construed in a manner to meet the practical necessities of the present.

After the Watergate scandal, many of the commission's reforms were adopted, including the Multistate Professional Responsibility Examination and establishment of bar disciplinary authorities in each state.

That commission, nicknamed the "Kutak Commission" after Omaha, Nebraska attorney Robert J. Kutak, drafted the Model Rules of Professional Conduct, which in 1983 after extended discussion and watering-down of the client perjury/organizational misconduct section, the ABA House of Delegates recommended succeed the Model Code of Professional Responsibility which the ABA (partly on the recommendation of Justice Lewis Powell) had proposed states adopt in 1969.

[55] Many states failed to adopt or enforce the model provisions relating to attorneys disclosing client misconduct, which after the Enron scandal, led Congress to pass the Sarbanes-Oxley Act in 2002.

The University of Texas's School of Law in Austin maintains an extensive collection (524 linear feet) of Clark's papers, including his Supreme Court files.

[59] A smaller collection of Clark's papers, primarily relating to his years as Attorney General, is kept at the Harry S. Truman Library in Independence, Missouri.