Only two states do not have religious exemptions to vaccination. One is West Virginia. In a recent court case, Jennifer Workman v. Mingo County Schools, the district court found in favor of a school district defending their right to exclude a child for refusing immunization.
The mother argued on constitutional grounds, citing the first, fifth and fourteenth amendments of the U.S. Constitution.
First Amendment argument
The first amendment includes freedom of religion:
Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof; or abridging the freedom of speech, or of the press; or the right of the people peaceably to assemble, and to petition the Government for a redress of grievances.
However, previous cases have decided
… that smallpox vaccination requirement does not violate free exercise of religion, because individuals’ “freedom to act according to their religious beliefs is subject to a reasonable regulation for the benefit of society as a whole
and,
‘the constitutional guaranty of religious freedom was not intended to prohibit legislation with respect to the general public welfare’
Equal Protection: Fifth and Fourteenth Amendment Argument
The fifth amendment amendment:
No person shall be held to answer for a capital, or otherwise infamous crime, unless on presentment or indictment of a Grand Jury, except in cases arising in the land or naval forces, or in the Militia, when in actual service in time of War or public danger; nor shall any person be subject for the same offense to be twice put in jeopardy of life or limb; nor shall be compelled in any criminal case to be a witness against himself, nor be deprived of life, liberty, or property, without due process of law; nor shall private property be taken for public use, without just compensation.
Fourteenth Amendment
Section 1. All persons born or naturalized in the United States, and subject to the jurisdiction thereof, are citizens of the United States and of the State wherein they reside. No State shall make or enforce any law which shall abridge the privileges or immunities of citizens of the United States; nor shall any State deprive any person of life, liberty, or property, without due process of law; nor deny to any person within its jurisdiction the equal protection of the laws.
Section 2. Representatives shall be apportioned among the several States according to their respective numbers, counting the whole number of persons in each State, excluding Indians not taxed. But when the right to vote at any election for the choice of electors for President and Vice President of the United States, Representatives in Congress, the Executive and Judicial officers of a State, or the members of the Legislature thereof, is denied to any of the male inhabitants of such State, being twenty-one years of age, and citizens of the United States, or in any way abridged, except for participation in rebellion, or other crime, the basis of representation therein shall be reduced in the proportion which the number of such male citizens shall bear to the whole number of male citizens twenty-one years of age in such State.
Section 3. No person shall be a Senator or Representative in Congress, or elector of President and Vice President, or hold any office, civil or military, under the United States, or under any State, who, having previously taken an oath, as a member of Congress, or as an officer of the United States, or as a member of any State legislature, or as an executive or judicial officer of any State, to support the Constitution of the United States, shall have engaged in insurrection or rebellion against the same, or given aid or comfort to the enemies thereof. But Congress may by a vote of two-thirds of each House, remove such disability.
Section 4. The validity of the public debt of the United States, authorized by law, including debts incurred for payment of pensions and bounties for services in suppressing insurrection or rebellion, shall not be questioned. But neither the United States nor any State shall assume or pay any debt or obligation incurred in aid of insurrection or rebellion against the United States, or any claim for the loss or emancipation of any slave; but all such debts, obligations and claims shall be held illegal and void.
Section 5. The Congress shall have power to enforce, by appropriate legislation, the provisions of this article.
The court found that equal protection was not violated:
But she presents no evidence of unequal treatment resulting from intentional or purposeful discrimination to support her claim; instead, all of the evidence is to the contrary.
The state health officer argued that equal protection was not violated:
I have never granted a medical exemption from the state immunization laws based on the reason being that the subject child or a relative has autism, or based on a posited connection between autism and vaccines, because neither reason is a recognized medical contraindication to these vaccines.
I am not aware of any instance in which the [West Virginia Board of Public Health] or any of its prior State Health Officers have ever granted a medical exemption to the immunization requirements appli-cable to school students based on a child or relative having autism, or based on a posited connection between autism and vaccines
The Court rejected all of Ms. Workman’s arguments.
The Court made it very clear that religious and philosophical exemptions are a a privilege, not a right. Most states do allow such exemptions, but, as the District Court noted in this decision:
Although most states have chosen to provide a religious exemption from compulsory immunization, a state need not do so.
Left Brain Right Brain 
Interesting ruling. I am wondering about the impact on the children, though. If the parents are adamant about not letting their children be vaccinated and that in turn means they cannot go to a public school, the children loose out twice: On their right to adequate medical care AND their right to an education. I am not sure what the best way would be out of that catch, but ultimately, the children end up marginalised.
There should be a price (beside increased risk of mortality and morbidity) for refusing to vaccinate your child. Private schools like Waldorf would welcome the little vectors with open arms. Home schooling is also an option. A couple of years back, Baltimore City Schools suspended students until they became compliant with the school system’s vaccination policy.