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No interference in church affairs. Since at least its 1872 decision in Watson v. Jones, the
Supreme Court has held that civil courts lack the competence or jurisdiction to decide
matters of theology, church discipline, ecclesiastical government, or the standards applied
to church members.29 This principle is most often applied to employment-discrimination
disputes, in which civil plaintiffs ask the state to gainsay the decisions of religious
organizations to hire, fire, promote, or demote ministers and others who formulate or
transmit religious doctrine. In this context, the doctrine is commonly called the “ministerial
exception” to whatever employment law is applied.30 More broadly, though, it is called
the “church autonomy doctrine,” and it protects a wide range of ecclesial decisions from
government interference, including decisions regarding the allocation of church
property.31
This doctrine has recently been invoked—and its limits have been disputed—in cases
where ministers have been charged with sexual abuse and their churches have been
accused of failing to oversee and manage those ministers and to report allegations of
abuse. Importantly, the church autonomy doctrine only limits liability or damages for
certain tort claims against religious organizations, when they are sued on theories
of vicarious liability for the acts of their ministers. The doctrine does not offer protection
against all (or even most) such claims.32 And, of course, the doctrine does not apply to
the abusive ministers themselves, and so does not insulate them from any liability, civil or
criminal. Nevertheless, since the sexual abuse scandal in the Roman Catholic Church in
2002, courts have applied these religious freedom principles less consistently, weakening
them more broadly.
No governmental religious discrimination. The Religion Clauses forbid governments at all
levels from targeting religious people or conduct for special disfavor, whether expressly or
covertly. In the jargon of Free Exercise Clause jurisprudence, this is described as the
requirement that laws be “neutral” and “generally applicable” with respect to religion. The
Establishment Clause provides a similar, if less frequently applied, prohibition against
government hostility to religion generally or to specific denominations. More concretely,
this means that laws may not discriminate on their face with respect to religion; laws that
are facially neutral may not be selectively applied against the religious; the government
cannot prohibit conduct because of its religious motivation; and people or groups cannot
be denied the protection of the law—or be excluded from participation in government
functions or from access to government benefits—based on their religious status or
views.33
No substantial burdens on religious exercise. The Free Exercise Clause also prohibits the
government from imposing nondiscriminatory, incidental burdens on religious exercise, but
this prohibition only applies under certain circumstances. The burden must be “substantial”
rather than a mere inconvenience, and must be applied in one of two types of cases. In the
first, the system for imposing burdens is highly discretionary or exception ridden, which
courts call a “system of individualized assessments.” Although the precise meaning of this
term is hotly contested, the classic “systems of individualized assessments” are zoning-
permit decisions, in which burdens are imposed on religious gatherings based on vague
criteria such as whether the gatherings are “consistent with the general plan” or
“consistent with neighborhood character.” The second type of situation in which
“substantial burdens” are forbidden is one where additional fundamental rights—such as
freedom of speech, of assembly, or to direct the religious upbringing of children—are

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