The Internal Revenue Service has attempted to clarify murky rules that govern the use of tax-exempt bonds to pay for university research facilities. The clarification, issued in a ruling on Tuesday, should help ease worries that conducting federally backed research in such facilities could jeopardize the bonds’ tax-exempt status.

Martha J. Frahm, a lawyer in Boston who helps nonprofit organizations structure their industry-sponsored research agreements, said she was pleased with the ruling. “This should foster additional industry investment in basic research at nonprofit institutions,” she said.

Bonds may be subject to taxation if any private group benefits from them with respect to research earnings. But because the Bayh-Dole Act gives the federal government some rights to research developments, and the federal government is considered a private entity in the bond market, some universities had feared that perceived preferential treatment would disqualify the tax-exempt status of bonds.

The Council on Government Relations, which represents research universities, had joined the National Association of Bond Lawyers in pressuring the IRS and the Treasury Department to clear up the conflict in the tax rules. The council reports that at least two universities had issued more-expensive, taxable bonds to build research facilities in order to avoid the potential problem.

Sen. Max S. Baucus, a Montana Democrat and chairman of the Senate Finance Committee, introduced legislation last May to expand the research and development tax credit. He also asked the IRS to make this “small fix” for tax-exempt bonds.

“In order to foster more basic research through federal-state-university partnerships,” Mr. Baucus said in a written statement, “we need to clarify that this provision of the Bayh-Dole Act does not cause these bonds to lose their tax-exempt status.” —Paul Fain