Though by his own admission he preferred to work for peace as an "independent human being without the aid of any organization," Pauling did, at least unofficially, affiliate himself with several peace groups throughout the 1950s. Among the more prominent of these ties was the National Committee for a Sane Nuclear Policy (SANE), a merged conglomoration of numerous local protest groups headed by Norman Cousins. Both Linus and Ava Helen spoke at numerous SANE-sponsored events, including a 1959 rally in New York at Carnegie Hall.

The Paulings also maintained a long association with the Unitarian Church and a close friendship with Stephen Fritchman, the minister of the First Unitarian Church of Los Angeles. Though Linus, at the age of eleven, had rejected the notion of a supreme being, a relationship with the Unitarians made sense to him for a number of reasons. In a 1962 letter Pauling noted:

"I am a member of the American Humanist Association and a member of the First Unitarian Church of Los Angeles. These memberships do not require a belief in God or acceptance of any other dogmantic, supernatural, or revelational beliefs. Both Humanism and modern Unitarianism are rational philosophies, which reject the mysticism and supernaturalism of the revealed religions, but are based upon the principle of service for the good of all humanity, of application of new ideas, of scientific progress, for the benefit of all man -- those now living and those still to be born. These organized religions (if it is proper to call them religions) encourage independence of thought and support ethical principles. I believe that association with them can be a positive factor in the development of a mature individual intellect."

Lastly, both Ava Helen and Linus were closely involved with a number of women-led peace groups, especially Women Strike for Peace and the Women’s International League for Peace and Freedom, for which Ava Helen served a three-year term as national vice-president.