This week marks the third anniversary of the Museum of Modern Art’s reopening in its sleek new building, and a birthday is as good a time as any to celebrate. The museum has the most stupendous collection of modern painting and sculpture in the world. It is where we go to reconnect with our roots, the place entrusted with presenting the genesis of modernism. MoMA is our fountain of youth, our Garden of Eden, our Promised Land. But all these things will not last much longer if this institution continues excluding women from the display of its permanent collection of painting and sculpture from 1879 to 1969, which lives on the fourth and fifth floors. Everything about this museum rides on the vibrancy and diversity depicted there, and MoMA is allowing that life to drain out. It is slowly turning the history of modernism into a procession of dead presidents and greatest hits, in effect making modern art a gated community and a state religion.

Each fall since MoMA’s reopening in November 2004, I’ve gone to these two floors, counted the number of artworks on view, tallied the number of women artists included, and then pitched a fit in print. So many women artists had come to light over the past few decades that MoMA’s reopening in 2004 became an enormous opportunity to alter its monolithic version of modernism. There was ample evidence that MoMA wanted to do so in 2000, when the permanent collection was totally rethought. Even the usually conservative chief curator of painting and sculpture, John Elderfield, admitted that previous MoMA installations had been "less real than ideal," adding that the museum now wanted to investigate "multiple narratives." It sounded as though the institution was on a slow but steady road to equal time.

That’s why the reopening brought such high hopes. On that Saturday in November 2004, the huge crowds wanted MoMA to be great. Opinions on the architecture varied but were primarily positive. (Yoshio Taniguchi’s building is handsome and essentially invisible; you can walk right past it and not know it, which may or may not be a good thing.) That first installation was the MoMA men’s club as usual, though you could make a case that it was an okay time for the old greatest-hits lineup to be trotted out one last time. (There were 415 works, excluding books, on view on the fourth and fifth floors, 20 of them -- less than 5 percent -- by women.) Either way, it was appropriate to temper one’s criticism. MoMA was learning how to deal with its new space, trying to get as many of the masterpieces on view as possible; we all needed to see them in their new house.

By the fall of 2006 -- after two years, and substantial tinkering -- there were 399 objects on view; 19 were by women, or 5 percent. Yet even this figure was misleading because MoMA had included three decorative objects by the estimable Marianne Brandt that weren’t, strictly speaking, in the painting-and-sculpture collection. The museum also slipped in a great Bridget Riley. But it was dated 1983-2002, well outside the closing date of the floor. So the real number was still around 3 percent.

Which brings us to the present, and after a great deal of art has been shuffled in and out of storage and rearranged, you can’t say MoMA isn’t sticking to its story. There are 28 Picassos on view, 22 Matisses, 15 Mondrians and 13 Rauschenbergs. On the fifth floor, MoMA has its Cézannes all in an astounding row. On the fourth floor, there’s a whole gallery of Ellsworth Kellys (constituting one of the museum’s "Focus" exhibits); the Johns-Rauschenberg-Twombly galleries have been revamped, as have parts of the Pop Art galleries. Best of all, the fourth floor now starts with six Willem de Kooning "Women."

Sadly, those slashing depictions are about the only women you’re going to see there. By my count, there are 400 works of art on these floors, 14 by women. That’s rock-steady at 3.5 percent, and includes the Bridget Riley again. Even if you give MoMA the benefit of the doubt and count only the number of artists on these floors, there are 137 -- 11 of them women. That’s 8 percent.

Not to sound like a broken record, but it has become bitterly clear that MoMA’s stubborn unwillingness to integrate more women into these galleries is not only a failure of the imagination and a moral emergency; it amounts to apartheid. Even the Met has integrated women into its 20th-century wing, hanging four Florine Stettheimer paintings and a room of ten Georgia O’Keeffes. Obviously, MoMA can’t invent modern masters and new Cubists. By my count, only about one percent of all the art up to 1970 in MoMA’s Painting and Sculpture Collection is by women. The people who run this institution are earnestly trying to do the right thing; I’m not declaring them sexist bigots. Nor am I a quota queen, advocating that women be allotted their 51 percent: Art history isn’t about fairness. Nevertheless -- and this is a vital point -- MoMA’s master narrative would not be disrupted if more women were placed on view. In fact, that narrative would come to life in ways it never has before, ways that would be revitalizing, even revolutionary. Ask yourself if hanging any of the following artists would really ruin the narrative espoused by the museum: Barbara Hepworth, Louise Nevelson, Louise Bourgeois, Joan Mitchell, Dorthea Rockburne, Yoko Ono and Florine Stettheimer. Or just take Alice Neel, a kind of American antihero (auntie-hero?) who painted in seclusion for nearly her whole life while raising children on her own in Spanish Harlem, and who arrived at an original figurative style that is simultaneously brooding, bizarre and Pop-ish. She’s one of the better painters of the mixed emotions of motherhood, and maybe the best painter of pregnant women who ever lived. Or MoMA could explore the work of Hilma af Klint, the Swede who fashioned mystic-looking alchemical diagrams and who arrived at pure abstraction more than five years before the great Kasimir Malevich. Even Frida Kahlo and Georgia O’Keeffe are missing. There’s no Mary Cassatt. I could list dozens more.

If the museum doesn’t own work by all of these artists, it needs to go shopping. For the hand-wringers who imagine this would trash the canon, I’ll note that cramming in 50 more paintings by women would still keep their presence below 16 percent. Of course, if MoMA removed some warhorses like Dine, Gottlieb and Kitaj at the same time, things could get really interesting.

Ideologies are fortresses; ideas blaze new territories. As many have said, MoMA needs to begin telling a more complex story of modernism, or it’ll be telling a story only it believes. Museums are not tombs where people go to simply stare at objects. They are places to participate -- places where things you don’t understand change your life. Museums have to not only defend the canon but also delve into and question it. They are guardians of history, but they’re also makers of meaning and metaphors. If a museum doesn’t continually nourish itself, it will die, and part of MoMA is dying.

But maybe only this part. Curators in other departments have bravely integrated women into exhibitions, with good results. This week will see the opening of Deborah Wye’s "Multiplex," a big group show of 72 works made from 1970 to the present. Not only does this exhibition contain 26 works by women; a lion’s share of the space will be devoted to large installations by Louise Bourgeois, Hanne Darboven and Nancy Spero. This summer’s "What Is Painting?" was more than a third women. The survey of Elizabeth Murray in 2005 was unevenly reviewed but a promising sign. The recent reinstallation of the photography collection includes excellent groupings of work by women, as does the current drawing show. The film-and-video and prints departments have long been virtually gender-blind. All this would resonate more if only MoMA weren’t fetishizing pure modernism on the fifth and fourth floors, trying to oversimplify the 20th century.

JERRY SALTZ is art critic for New York Magazine, where this article first appeared. He can be reached at jerry_saltz@newyorkmag.com