Most European systems of church-state relations are based, explicitly or implicitly, on the principle of cooperation of the state with religion; and many states articulate such cooperation through multi-tier systems, i.e., systems that grant differentiated legal statuses to religious communities depending on a number of factors, often related to their social rooting. These systems raise the question of how to reconcile the diversity of legal statuses of religious communities with the principle of equality, which on the one hand requires avoiding discrimination (i.e., unjustified legal differences) and on the other hand demands treating differently social realities that are different. This paper is composed of three parts, each of them with a different presenter. The paper will address this issue in two different and interrelated contexts. One is the Spanish constitutional system as developed by legislation and case law, with specific reference to: a) the situation of religious communities that have registered in the Registry of Religious Entities, analysing the effects of registration in comparison with expressions of state cooperation through specific channels designed for communities with broader social roots; b) the situation of religious communities that have a cooperation agreement with the state and those others that meet the legal requirements to reach such agreements but have not been able to do so due to political circumstances. The other context is the case law of the European Court of Human Rights, which for some time has been holding that the European Convention does not oblige states to cooperate with religious communities; but, if they decide to do so, they must design such cooperation with scrupulous respect for the principle of equality enshrined in article 14 ECHR.