Ginzburg was an avowed atheist, both under the militantly atheist Soviet government and in post-Communist Russia when religion made a strong revival. He criticized clericalism in the press and wrote several books devoted to the questions of religion and atheism. Because of this, some Orthodox Christian groups denounced him and said no science award could excuse his verbal attacks on the Russian Orthodox Church. He was one of the signers of the Open letter to the President Vladimir V. Putin from the Members of the Russian Academy of Sciences against clericalisation of Russia.