Whether to strip Blue Cross and Blue Shield of their historical tax-exempt status is one of the important, but less publicized, puzzles House and Senate conferees must unravel as they begin considering a final version of a tax-revision bill this week.

The House tax bill, which was passed in December, effectively would revoke tax exemptions enjoyed by the 79 Blue Cross and Blue Shield health insurance plans. The recent Senate legislation kept these exemptions, which officials at the health insurance plans say are critical to their ability to provide affordable coverage to millions of people in the high-risk category.

Collectively, the Blue Cross and Blue Shield plans represent the single-largest share of the health insurance market, but this share has been eroded during the years by commercial insurers, by health maintenance organizations and by employers who switched to self-insure. In 1985, the Blue Cross and Blue Shield plans' market share was estimated at 27 percent compared with 42 percent in 1975. Enrollment in the plans now totals 77.5 million people.

Commercial health insurers and others who favor changing the law argue that the Blue Cross and Blue Shield plans have come to behave like for-profit insurers, and, thus, the tax exemptions give them an unfair competitive advantage.

This position received a boost last week by the release of a General Accounting Office report concluding that there are "more similarities than differences" when comparing important features of the Blue Cross and Blue Shield plans and of the commercial plans.

Blue Cross and Blue Shield officials, by contrast, contend they provide a source of health-care coverage for millions of Americans who could not obtain insurance from commercial carriers. They say that without the Blue Cross and Blue Shield tax break, this coverage would be much more expensive and difficult to obtain.

"It means that more people are going to fall through the cracks," Mary Nell Lehnhard, vice president for government relations at the Blue Cross and Blue Shield Association, said this week. "Some people who are getting insurance now would not be able to afford it anymore."

Congressional officials have estimated that $1.7 billion in revenue would be generated over five years by eliminating the tax break for the Blue Cross and Blue Shield plans. Lehnhard said the figure is overblown.

The revenue figure is relatively small compared with what other provisions of the proposed tax bills would generate. But the issue has drawn interest because eliminating the tax break would reverse one of the oldest traditions in the health-insurance industry and would add to market pressures facing Blue Cross and Blue Shield plans.

Blue Cross and Blue Shield plans emerged in the 1930s as the nation's first form of health insurance and were recognized by the Internal Revenue Service as social welfare organizations.

As such, these plans have been considered exempt under IRS regulations from paying federal income taxes. The regulations allow tax exemptions for nonprofit groups that operate exclusively to promote social welfare, although they do not allow exemptions for these groups to run businesses in a similar manner as for-profit organizations.

With the growth of a more competitive health insurance market, many critics have questioned the exemptions for the Blue Cross and Blue Shield plans. Late last year, House tax writers, led by Rep. Fortney H. (Pete) Stark (D-Calif.), chairman of the Ways and Means subcommittee on health, eliminated the exemptions in the revision package.

Senate tax writers kept the Blue Cross and Blue Shield tax break, and 42 senators signed a resolution introduced last month urging that the tax exemptions be maintained without modification. Supporters the current tax break include Sen. Bob Packwood (R-Ore.), chairman of the Finance Committee.

But the hotly debated issue resurfaced last week after the General Accounting Office, a watchdog agency for Congress, released a study showing, among other matters, that two-thirds of 129 high-risk persons insured by Blue Cross and Blue Shield plans could get insurance with commercial carriers.

Stark, who requested the study, said the report "supports what I think we have known all along: Blue Cross and Blue Shield should be taxed."

But the GAO study drew heated criticism from Blue Cross and Blue Shield officials, who charged it contains "serious inaccuracies and major omissions."

The federal tax exemption is "one of the factors that enables Blue Cross and Blue Shield plans to provide health insurance coverage to high-risk applicants at affordable prices," said Bernard R. Tresnowski, president of the Blue Cross and Blue Shield Association.

Blue Cross and Blue Shield officials said the major burden of revoking the tax exemption -- in the form of increased premiums or the possible denial of coverage -- would fall on individuals who must purchase health insurance on their own rather than those who obtain insurance through group policies offered by their employers.

There are roughly 11 million people around the nation with individual coverage, according to Blue Cross and Blue Shield officials. In the Washington area, this includes 30,000 individual subscribers under age 65, a spokesman said.