[310] The Ole Miss riot of 1962 left two civilians dead and 300 people injured, prompting President Kennedy to send in 3,000 troops to quell the riot.[311] Meredith did finally enroll for a class, and Kennedy regretted not sending in troops earlier. Kennedy began doubting as to whether the "evils of Reconstruction" of the 1860s and 1870s he had been taught or believed in were true.[304] The instigating subculture during the Ole Miss riot, and many other racially ignited events, was the Ku Klux Klan.[312] On November 20, 1962, Kennedy signed Executive Order 11063, which prohibited racial discrimination in federally supported housing or "related facilities".[313] Despite this, in Boston, the Boston Housing Authority (BHA) Board would continue to actively segregate the public housing developments in the city during the John F. Collins administration (1960–1968), with BHA departments engaging in bureaucratic resistance against integration through at least 1966 and the Board retaining control over tenant assignment until 1968.[314]
Both Kennedy and Robert Kennedy were concerned about King's ties to suspected communists Jack O'Dell and Stanley Levison. 