A lawsuit now in court could wreck a long-held tradition.

Before there was a First Amendment, there were chaplains in the U.S. Army, ministering by popular demand among militia from their own hometowns during the Revolution. They were paid $20 a month by the fledgling government, and their status went unchallenged even after the Constitution was amended to prohibit state establishment of religion.

Today, there are 3,347 ordained men and women in uniform, earning salaries equivalent to other officers. A case pending in U.S. District Court in Brooklyn, however, could leave the chaplains wholly dependent on their churches for financial support and strip them of their officer rank.

The case is a taxpayer’s suit brought by Joel Katcoff and Allen M. Wieder, who began the project in 1979 as Harvard Law School students. They targeted the U.S. Army, the largest of the armed forces with 782,000 active-duty soldiers. They allege that the government “by design and appearance, lends its prestige, influence, and power to organized religion.”

At issue is a direct conflict between the Constitution’s guaranteed free exercise of religion and the prohibition against state support of religion. In the military, the absence of pastoral counseling, worship, fellowship, or Bible study—all functions of the chaplain corps—would deprive GIs of opportunities to practice religion. But Katcoff and Wieder counter that those needs should be met privately by churches or mission-sending groups, and that tax dollars should not line clerical pockets.

Churches clearly have the most at stake financially, because each chaplain is estimated to cost the government more than $100,000 per year for salary, programs, and administrative costs. The comparison is inadequate, ...

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