Six years on, that right is being eroded. Free worship is under attack again, not this time by a bullying central party but by Russia's scores of far-flung regional governments, where democratic reforms have yet to supplant Communist-era attitudes and where many of the old apparatchiks remain in power.
A tranche of regional laws is gradually being introduced restricting the rights of minority churches, in an effort to protect the Russian Orthodox Church, which is closely linked to the state, from outside competition. Provincial government posts are being created to allow officials to keep an eye on religious activity.
Each separate development pales by comparison to the wild excesses of the Communist Party or Stalin during Soviet times, when thousands of churches were shut and distributing Bibles could land you in a labour camp. But, taken together, they add up to a disturbing picture.
The issue has been brought to light by the Keston Institute, a respected independent research centre based in Oxford, which was in the forefront of the campaign against religious repression under Soviet rule. Research by its Moscow representative, Lawrence Uzzell, estimates that a quarter of Russia's 89 regions and republics have adopted measures that restrict the right to freedom of worship.
In some regions, local officials have taken powers which allow them to regulate foreign and domestic clergy and even to impose a ban if they disapprove of their activities. These include laws stating that missionaries must have an annual certificate of accreditation.
In other cases, local authorities, which still own most large civic buildings in provincial Russia, can now legally forbid religious groups from renting their properties for church services. There are laws denying registration to churches which the authorities decide are committing such vague offences as "promoting disobedience to state authorities" or "encouraging citizens to refuse to carry out their civic or family obligations".
Such laws not only contradict the 1990 law, they are also flagrantly ignore the Russian constitution, adopted three years ago, which guarantees universal religious freedom. "The rapid spread of such measures, and the courts' failure to curb them, suggests that Russia is not even trying to become a state governed by law," Mr Uzzell said.
Despite widespread secrecy among regional governments - some of which refuse even to reveal the text of their legislation - he has assembled specific examples. In Sverdlovsk, individuals or organisations who provide meeting places for missionary activities are required to tell the local authorities. In Tver, an executive order has been issued denying accreditation to "structural sub-units of foreign religious organisations located outside the border of the Russian Federation" - a catch-all clause that could include those with deep roots in Russia, such as Catholicism.
So why is it happening? One explanation is a fear of cults, which have burgeoned since the fall of the Soviet Union. But it has more to do with the reflex habit of Soviet-era apparatchiks to regulate religion in the interests of the state. That, and the nationalist-leaning Orthodox Church's anxiety to maintain its position in a country where there are now a million non-Orthodox believers.
"The church is paranoid about foreigners," Mr Uzzell said. "The spiritual expansion of the West is seen as part and parcel of its political and economic expansion. Just as in Soviet times, they see McDonald's executives, Baptist missionaries and western diplomats as part of one monolithic structure."
The Orthodox Church is strongly rumoured to be attempting to push legislation through parliament recognising only four official religions: Orthodoxy, Islam, Buddhism, and Judaism.