The study, from the International Humanist and Ethical Union (IHEU), showed that "unbelievers" in Islamic countries face the most severe - sometimes brutal - treatment at the hands of the state and adherents of the official religion.
But it also points to policies in some European countries and the United States which favor the religious and their organizations and treat atheists and humanists as outsiders.
The report, "Freedom of Thought 2012", said "there are laws that deny atheists' right to exist, curtail their freedom of belief and expression, revoke their right to citizenship, restrict their right to marry."
Other laws "obstruct their access to public education, prohibit them from holding public office, prevent them from working for the state, criminalize their criticism of religion, and execute them for leaving the religion of their parents."
The report was welcomed by Heiner Bielefeldt, United Nations special rapporteur on freedom of religion or belief, who said in a brief introduction there was little awareness that atheists were covered by global human rights agreements.