He was raised a Conservative Jew and attended religious services, yet later quipped (in a speech made before Freedom From Religion Foundation[3]) that "the Orthodox consider me to be the worst enemy they've had - since Haman in the Purim story!"
In that period he wrote several books on religious freedom, the separation of religion and state, and the corresponding decisions of the US Supreme Court.
After 1964 he also served AJC as special counsel, and did legal work on behalf of other groups, including the Committee for Public Education and Religious Liberty.
By account of contemporaries, for most of the 1950s Pfeffer remained the dominant individual force in managing the flow of church-state litigation in state and federal courts intended to test the constitutionality of the religious oath requirement, school, prayer, and Bible reading - a role Pfeffer retained well into the early 1970s.
[5] While he was with AJC, Pfeffer argued cases before the Supreme Court and wrote numerous legal briefs.
In 1961 he attained wide attention when he argued the case of Torcaso v. Watkins before the Supreme Court that a provision in the Constitution of Maryland requiring an express belief in the existence of God as a condition for the admission to holding of a public office, was unconstitutional.
In defending atheist Roy Torcaso's case challenging a religious test in Maryland to become a notary public, Pfeffer wrote that "there are religions which are not based on the existence of a personal deity."