The school district filed a motion to dismiss the complaint, arguing the DHHR should have been a defendant, and lawsuits against state agencies must be filed in Kanawha County.
The state Attorney General's Office filed a motion to allow the DHHR to intervene, and another asking the judge to dismiss because it was filed in the wrong county.
West Virginia has some of the nation's strictest limits on exempting children from vaccines required before they can attend school, and some parents have been lobbying the Legislature to change that.
Public health officials, however, warn that the state already suffers low immunization rates against diseases such as polio, whooping cough and measles.
All states, including West Virginia, allow school-bound children to skip immunizations for medical reasons. But while 48 states also permit exemptions on religious grounds, West Virginia and Mississippi do not.
Phil Hudok has made headlines challenging state laws before. In 1999, he was fired from his teaching job in Randolph County for refusing to require his students to wear bar-coded identification badges. He was later reinstated after a circuit judge said the school board had made no attempt to accommodate his religious beliefs.
Then in 2008, the West Virginia Division of Motor Vehicles started a paper-based pilot program to keep driver's license photos out of a computer database to accommodate Hudok and others who believe digital storage is a "mark of the beast" that evokes biblical prophecy.
Hudok argued that bar codes and digital storage of photos are a way of numbering people, which they liken to a warning in the Bible's book of Revelation about a "mark of the beast" indicating the arrival of the Antichrist.