A trial is to begin here on Wednesday morning to determine whether a Jewish couple can deduct the cost of religious education for their five children, a tax benefit they say the federal government has granted to members of just one religion, the Church of Scientology.

The potential ramifications are huge, for a ruling in favor of the couple could affect the millions of Americans who send their children to religious schools of all types. At stake is whether people of all religions can deduct the cost of religious education as a charitable gift, as Scientologists are allowed to do under an officially secret 1993 agreement with the Internal Revenue Service.

That agreement came despite a 1989 Supreme Court ruling denying tax deductions for money paid in fees set by the Church of Scientology for its ''auditing'' and ''training'' services. The Supreme Court decision said the money did not qualify for the charitable gift deduction because it involved a fixed price and was akin to a fee for a service.

The couple, Michael and Marla Sklar of Los Angeles, originally took the I.R.S. to court after being denied $2,080 in 1993 deductions for religious education for their children. They lost that case, in which Mr. Sklar, a tax accountant, represented himself at trial. The couple appealed, and three judges on the Court of Appeals for the Ninth Circuit ruled against them two years ago. But one judge also took the unusual step of suggesting further litigation that would better define the issues.