For the first time in its history, the National Collegiate Athletic Association has begun punishing colleges for their athletes' academic failure.
The association announced  Wednesday that 99 teams at 65 Division I colleges  would forfeit at least part of an athletic scholarship in the next year because of academic underperformance by athletes. (The total could rise slightly because eight universities are still appealing proposed penalties.) Ninety of the affected teams are squads for men, and 61 of them are in the sports of football, men's basketball or baseball. Several universities, including Florida A&M  and New Mexico State  Universities, and the Universities of Hawaii at Manoa  and Toledo,  had multiple teams punished.
The penalties are part of a much broader, several-year effort  by the NCAA to hold colleges more accountable for their athletes' academic progress. At the core of the system is a measurement tool called the Academic Progress Rate, which is designed to provide a "real time" look at how individual teams are faring at keeping their scholarship athletes on track to a degree.
The message is "simple," said Walt Harrison, president of the University of Hartford and chairman of the NCAA's Executive Committee. "Recruit students who are capable of doing the academic work at your institution, and give them the support they need to succeed. The APR measures how well you're doing at those two things."
The message might be simple, but explaining how the academic progress rate works isn't.
Each scholarship recipient on a given team’s roster at the start of an academic year can receive a maximum of two points per term: one for finishing that term having met the NCAA’s newly toughened academic progress standards and the institution’s own academic rules, and another for remaining enrolled at the institution. So an athlete who stays eligible and enrolled at the institution for both semesters of a given year gets a total of four points. An athlete who was academically eligible but chose to leave the college (to transfer or to play professionally, say) in the middle of the spring semester would get three points, while a player who flunked out in the first semester would get zero points for the year.
A team’s academic progress rate (or APR), then, is calculated by dividing the total number of points earned by the players on its roster for the year by the total number of points possible, then multiplying by 1,000. So a team with 10 athletes, all of whom stay eligible and remain at the college, would have a perfect score of 1000. A 10-person team that had one player flunk out in the first semester would have a score of 900 (36 points divided by 40 points times 1,000).
Beginning in the 2007-8 academic year, the NCAA will begin imposing what it calls "historical" penalties -- which could ultimately include bans on postseason competition -- against teams that consistently fail to perform. But to kick the system into gear and "begin to change behavior," as Myles Brand, the NCAA's president, put it in a telephone conference Wednesday, the association has introduced its first set of "contemporaneous" scholarship limitations.
Under this approach, a team loses a scholarship if its academic progress rate for the previous year falls below 925 (with certain exceptions, to be explained below) and if an athlete on that team left the institution without being in good academic standing (in other words, if he or she failed out). Teams can lose up to a maximum of 10 percent of their total scholarship allotments, which in the case of Division I-A football can be as many as nine scholarships. The cutoff of 925 is meant to equate roughly to a federal graduation rate of 50 percent or to a rate of 60 percent on the NCAA's new Graduation Success Rate,  which it prefers to use.
Of the 6,112 teams in Division I, 943 had APR scores that fell below the 925 threshold in the 2004-5 academic year. But more than 700 of them qualified for one of two exemptions that NCAA leaders instituted to soften the initial impact as it phases in the new standards. One -- a "squad size adjustment,"  which the association equates to a margin of error in public opinion polling -- allows teams with fewer athletes to fall below 925 by varying amounts. (The squad size limitation will diminish before eventually disappearing in 2007-8, and NCAA officials warned that many more teams -- up to 40 percent of squads in football, basketball and baseball -- could be susceptible to penalties when the size adjustment ends.)
The other mitigating factor, which Kevin Lennon, the NCAA's vice president for membership services, said had benefited 63 teams, minimized or eliminated scholarship reductions for teams at institutions based on their "missions" -- for instance, if they tend to serve large numbers of academically underprepared students generally or have very low graduation rates for all students.
When those exceptions were taken into account, 215 teams fell below the 925 cutoff, including 178 men's teams and 37 women's teams. Of those, though, 99 had at least one player who failed academically, and hence required the team to forfeit a scholarship either this year or in the 2006-7 academic year. (A list of the affected institutions appears here.) 
Some patterns emerge in the sports and colleges affected. Disproportionate numbers of baseball programs lost at least one scholarship, for instance, including high profile teams at California State University at Fresno, Oklahoma State University and the Universities of Tennessee at Knoxville and Texas at Austin. In addition, nine historically black universities were among the 65 Division I colleges that faced scholarship reductions, which is significantly more than their representation among all Division I institutions. Five sports at both Florida A&M and Prairie View A&M Universities lost scholarships, for instance. Brand and other NCAA officials said both of those situations concerned them.
Some individual institutions appeared to fare poorly, too. At New Mexico State, for instance, the football, men's basketball and baseball teams all lost scholarships (with football losing six and basketball losing the maximum of two); institution officials did not return telephone calls seeking comment, but they told ESPN.com that they had appealed the penalties unsuccessfully, citing significant turnover in the ranks of coaches and sports administrators.
Kent State University also unsuccessfully appealed its loss of two men's basketball scholarships, which Laing Kennedy, the athletics director, said had occurred because of an "anomaly" last year in which several players left the team under unusual circumstances. "It's ironic because our graduation rate has never been higher, and we could have made different decisions that would have made the athletes stay instead of letting them leave," said Kennedy. "But once our initial appeal was turned down, we just said, 'We can deal with this. We support this rule, so let's move on.' "
Other institutions took big hits, too. Among colleges that play football in Division I-A, the NCAA's top competitive level, only Temple University lost the maximum number of nine scholarships, while seven Division I-AA institutions -- Florida A&M, Jacksonville State, Murray State, Nicholls State and Stephen F. Austin State Universities, and the Universities of Tennessee at Chattanooga and at Martin -- forfeited the maximum six scholarships at that level.
Eight other institutions are still negotiating with the NCAA over possible scholarship losses. They are: Arizona State, Northern Arizona, San Diego State, San Jose State, Texas A&M and Tulane Universities, and the Universities of Arizona and Kansas.
Four teams at California State University at Sacramento  -- baseball, football, men's basketball and men's and women's track and field -- lost at least part of a scholarship (though baseball was one tenth of one.). Its athletics director, Terry Wanless, who took over the sports program in 2002, said that the university had, in retrospect, "maybe picked the wrong time" to upgrade its athletics department both athletically and academically. He has replaced eight coaches in three and a half years there, with the inevitable fallout of some players choosing to transfer out, and the university has also "eliminated kids from our program that weren't so strong" academically.
The result, Wanless said, is that the 2003-4 and 2004-5 academic years on which the new APR scores are based make Cal State Sacramento look bad. "In our attempts to make the program more competitive, both athletically and academically, and to make changes in leadership roles for the betterment of the program, those changes brought about changes in stud athletes" that hurt academic progress results.
"But the good news," he said, "is that while we are suffering from that change, we are also showing progress because of that change." The APR scores of seven of the university's nine men's teams improved from 2003-4 to 2004-5, and the department's overall average score rose by 29 points.
That is just the sort of movement that Brand, the NCAA's president, said the new academic requirements were designed to bring about. "Our phased-in approach to the APR and the accompanying penalty structure are changing the way the Division I athletics community thinks about student-athlete academic performance."