It's a sneaky little bug, waiting for weeks to show up after a person has been infected. So it was quite a while between the time that doctors recognized its existence and the time they began to connect it with sexual activity.

And even then, because it produces few symptoms in women -- it's "silent," as the doctors say -- and because it was particularly difficult to grow in the laboratory, it got away with a lot of damage before the researchers caught on to its troublemaking potential.

It is chlamydia, technically Chlamydia trachomatis, a microorganism barely known a decade ago, but which today holds the dubious distinction of being the number one sexually transmitted disease in this country -- ahead of gonorrhea, ahead of genital warts, ahead of herpes, way ahead of syphillis.

According to Bruce Shephard, obstetrician/gynecologist and coauthor (with Carol Shephard) of "The Complete Guide to Women's Health," there are about 3 million new chlamydia cases every year in the United States, with some estimates as high as 10 million. It is especially common on college campuses, where it surpassed gonorrhea several years ago.

Until recently, most scientists believed that gonorrhea was the single principal cause of pelvic inflammatory disease (PID) with, as Shephard puts it, "an assortment of weird-sounding microorganisms" accounting for the rest.

Now, however, it is widely believed that chlamydia is responsible for nearly 50 percent of the million cases a year of PID, right on the heels of gonorrhea, the better known venereal disease. Shephard believes that the cause-and-effect evidence is still lacking for an absolute indictment of chlamydia, but "there is an association. Patients with chlamydia are at increased risk of PID."

PID, in turn, can cause chronic pelvic pain and infertility. And, because it can scar the fallopian tubes which transfers eggs from the ovary to the uterus, PID increases the possibility of an egg becoming caught and fertilized in the tube -- resulting in a potentially life-threatening ectopic pregnancy.

"These three health problems," says Shephard, "are sizable and increasing, and chlamydia seems to be one of the reasons." There are approximately 1 million cases of pelvic inflammatory disease diagnosed each year, with some 200,000 hospitalizations, 10,000 infertilities and several thousand related ectopic pregnancies.

The babies of pregnant women infected with chlamydia -- and studies, says Shephard, indicate that probably 10 percent of pregnant women are infected -- are at risk of being born with an eye infection or pneumonia.

The pneumonia related to chlamydia is the most common form in infants up to about 4 months old, he says. It also has been linked to stillbirths and miscarriages, although here again, says Shephard, the evidence is not yet entirely conclusive.

Nevertheless, he expects that routine screening will be recommended soon by public health officials. Chlamydia is not yet required to be reported, but screening, especially of pregnant women, "would be a nice simple thing to do."

Other factors contributed to the late recognition of the magnitude of the chlamydia problem, not the least of which is the still-prevalent attitude of both doctor and patient to sexually transmitted diseases. Even with all the purported sexual freedom of the '80s, nobody wants to admit that he or she has one of those, you know, one of those dirty little social (shhh) things.

Physicians, confirms Shephard, still are reluctant to probe too deeply into the sexual habits of their patients. And how many patients are ready to discuss multiple sex partners with their doctors or anybody else?

Possibly the major reason chlamydia went undiscovered so long was its own character. It often comes along with gonorrhea -- social diseases travel in packs, as a rule -- but chlamydia is resistant to the penicillin that knocks out most gonococcal organisms, so even when the gonorrhea is gone, the chlamydia may be lingering on.

Moreover, until two new tests became available within the last year, chlamydia was difficult to diagnose, and even when lengthy laboratory tests were undertaken, it did not always show up, even when it was present in the patient.

Chronic pelvic pain in women was, says Shephard, often misdiagnosed as "spastic colon" or "stress related" or "something psychological" because even with X-rays and laparoscopies, the chlamydia organism remained elusive.

In men, symptoms of chlamydia are burning urination and penile discharge -- easily mistaken for gonorrhea or prostate infection, with the latter being the "nicest" and most common misdiagnosis. The incubation period is longer than gonorrhea's two to five days and this is, says Shephard, "a subtle but important point."

That means physicians often don't identify a chlamydia infection until it is well established, which makes it harder to treat, he says. It also means that when multiple partners are involved, chlamydia's one- to three-week incubation may make identification of the partner that much more difficult.

Chlamydia responds well to courses of tetracyclines (doxycycline, for example) and to erythromycin. Only recently, the Centers for Disease Control has recommended that gonorrhea patients be treated with one of those drugs as well as the drug of choice for the gonorrhea -- "double coverage" as a matter of routine. (Tetracyclines, however, are not recommended for pregnant women.)

"Being able to communicate freely with your partner," says Shephard, "is a good first step to early identification and treatment."

He also suggests that people with multiple sex partners "consider a contraceptive that protects against venereal disease." These are:

Barrier contraceptives like the diaphragm.

Spermacide jellies and creams. (Their efficacy was established a few years ago, notes Shephard, in clinical trials on prostitutes in Nevada, the only state where prostitution is legal.)

Condoms. "These," says Shephard, "are best of all." It doesn't take The New England Journal of Medicine to prove it, he says -- just everyday experience going back to the World War II GI.