In contrast to Ms. Morcroft’s lonely fight in Tallahassee, Pastor Warren, who declined to be interviewed for this article, had a host of allies when he went to battle to defend the special tax deduction for housing expenses of clergy members. Ultimately, the allies included both houses of Congress and the president of the United States.

The Housing Exemption

The one small passage in the vast federal tax code that originally conferred the housing-expense exemption on clergy members did not cap the deduction. But in 1971, the Internal Revenue Service limited it to the “fair market rental value” of the furnished home, utilities included.

During a routine audit in 1996, according to court documents, the I.R.S. decided that Pastor Warren’s housing deduction exceeded the rental value of his new home on Via Del Sol in the rugged Trabuco Canyon, southeast of Los Angeles.

That’s when the fireworks began.

Pastor Warren, who gives 90 percent of his considerable income to charities, later explained in an open letter to other ministers that he decided to sue because the housing allowance was the only way small churches could pay their pastors enough to live — and he knew that those ministers could not fight the I.R.S. as he could.

The deduction, usually called the parsonage exemption, is available to ministers, rabbis and other clergy members of all faiths working at houses of worship. It allows them to live in congregation-owned housing without being taxed on the imputed value of their free housing, as almost all other employees are when they live in company-paid housing.

Since 1954, the provision had also shielded clergy members from taxes on the entire portion of their paycheck designated by their congregations as a housing allowance, whether they spent it on renting an apartment or buying their own home. But the rules the I.R.S. adopted in 1971 limited the deduction to the smallest of three amounts: the “fair market rental value” of the home, the housing allowance paid to the minister or the minister’s actual housing expenses.

Image TAX BREAKS FOR THE CLERGY Saddleback Church, in Lake Forest, Calif. The churchs founder fought for tax breaks for clergy members, citing their service to society. Such breaks help both poorly and well-paid ministers, but are not available to low-paid teachers or secular charity workers. Credit... Monica Almeida/The New York Times

That ruling lighted the long fuse that, decades later, propelled Pastor Warren into court.

It took four years — and far more of Pastor Warren’s money than the $55,300 disputed in the audit — but on May 16, 2000, the United States Tax Court struck down the I.R.S.’s cap and ruled that clergy members could deduct “the amount used to provide a home,” however much that might be.