It's bad enough to have to cope with the intestinal beasties that cause travelers' diarrhea when visiting a foreign country, but somehow it is adding insult to injury to come home with an assortment of alien bugs, bacteria and parasitic protozoa tagging along in your gut.

Travelers' diarrhea, as last month's National Institutes of Health consensus development conference noted, is most often a three-day affair more inconvenient than disabling. But for some luckless wanderers, things go from bad to worse.

Sometimes the onset of the illness can be days, weeks, even months after returning home from a trip, and its connection to something picked up on the travels may be missed. Some of these critters are rare indeed in this country and are often missed by physicians who practically never encounter them. As tropical medicine specialist Dr. Martin S. Wolfe told colleagues on the NIH panel, "they can get lost in the vast garbage can of 'irritable bowel syndrome.' "

As a general rule, most of these unpleasant little things that make it past customs are the excess baggage of the Peace Corps volunteer or the businessman or diplomat who has been out of the country for a matter of months, rather than weeks. But a good infection can develop on one- or two-week sojourn as well.

Take the case, for instance, of a man who returned recently from a visit to southern Africa. Upon his return he began having fever and chills, sweats and headaches. He was referred to Wolfe, director of the Traveler's Medical Service of Washington. Wolfe also serves as travel medicine consultant to agencies such as the State Department, the World Bank and the Peace Corps.

Wolfe looked at the symptoms, he recalls, which by this time also included a mild rash.

It looked, he thought, like a rickettsial illness. Rickettsia are bar-shaped microorganisms that are generally transmitted by the bite of a mite or tick and cause illnesses in humans such as Rocky Mountain Spotted Fever.

"Tell me where you went on this trip," he asked the patient. "Get any bites?"

In fact, the patient told him, he had spent time in the African bush and had been bitten "by a variety of ticks and mites."

"I think you have African tick typhus," Wolfe told the traveler, "and if you do, you'll respond very well to a short course of tetracycline." He was better the next day, recalls Wolfe, and subsequent blood tests confirmed the diagnosis. African tick typhus is not as serious as Rocky Mountain Spotted Fever, says Wolfe, "but untreated, it can occasionally cause fatalities."

"As it turned out," says Wolfe, with considerable satisfaction, "a few of his colleagues in New York City had a similar illness. When he told them what he had, they went to their doctors and on the basis of his already-treated case, their own doctors were able to diagnose the others. They all had it. They all got well. It was very gratifying."

Admittedly, African tick typhus is pretty rare, but Wolfe sees a few patients each month who acquired what they thought was a routine turista that simply wouldn't go away.

Treatment often depends on which organism is causing the trouble, but tracking them down is usually left to low-ranking laboratory technicians who are often undertrained for the work, which is widely considered undesirable. To counter this, Wolfe established his own parasitology lab where technicians can do the often tedious procedures designed to find the cause of unusual infections.

Some of the bacterial infections, including the ubiquitous E. coli along with shigella, campylobacter and salmonella, can last longer than a few days and cause considerable distress. However, most of the longer-lasting problems are caused by parasites, Wolfe believes, from one-celled protozoa to worms.

Among these are:

* Giardia lamblia. This is a parasite that afflicted travelers to the Soviet Union in the 1970s and is now seen in travelers returning from Mexico, South America, South and Southeast Asia and the Middle East. It has been seen more and more among U.S. hikers who drink untreated water from streams that have been contaminated by the feces of animal carriers. Beavers are considered prime carriers. Symptoms are explosive abdominal distress sometimes accompanied by chills and low-grade fever, weight loss and fatigue. Drugs for treatment are available, but its diagnosis is sometimes missed.

* Amoebae. These one-celled critters can cause a variety of ills ranging from life-threatening (but relatively rare) amoebic dysentery to no symptoms at all in persons who carry (and can transmit) the amoebic cysts. Amoebiasis can be acquired worldwide and its symptoms may be acute or chronic. It can be treated, but is often missed.

* Sprue. This is a rather mysterious and rare ailment that causes a type of intestinal malabsorbtion. Its symptoms often resemble giardia, but they also have been mistaken for irritable bowel syndrome. Researchers believe it is caused by an organism because it responds to tetracycline (as well as folic acid, a B-complex vitamin), but no organism has even been isolated.

* Worms. Some are acquired through food and water, others through the skin by walking barefoot in areas where they exist. These include roundworms, whipworms and other parasites that can cause neurological or intestinal problems, depending on where they congregate. Virtually all can be treated, some more easily than others.

One fairly common worm parasite is carried by snails, and most human victims acquire it by swimming in fresh water ponds or lakes, where the snails abound. The infestation is called schistosomiasis and is found, says Wolfe, in some Caribbean islands and parts of South America, Africa and the Middle East. Because people sometimes do not become ill for weeks, the cause of the condition can be missed. The initial acute illness can include fever, wheezing and abdominal pain. Abdominal pain, low-grade fevers and weight loss may follow. Once diagnosed, says Wolfe, it is quickly and easily treated.

Wolfe recommends that travelers to areas where malaria is endemic begin a course of prophylactic drugs that must be taken until four full weeks after the traveler's return home. Some malaria strains are now resistant to some forms of treatment, so prevention is by far the most sensible way to go. (Malaria-carrying mosquitoes bite only at night, so many city-only travelers may simply avoid them by staying inside, Wolfe says.)

Finally, because hepatitis A is common in underdeveloped countries, Wolfe suggests receiving gamma globulin shots against hepatitis A before going into the country and to repeat them at six-month intervals, if the journey warrants.

A travel writer for the British newspaper The Guardian wrote recently that the air in Mexico City was so polluted "one could get hepatitis just by breathing." It may not be quite that bad, say the experts, but it never hurts to be prepared. Resources

Travelers can get information about and treatment for diseases acquired in foreign countries from the following centers:

* Traveler's Medical Service and Associated Parasitology Laboratory, 2141 K St. NW, Suite 408, Washington, D.C. 20037. 466-8109.

* International Health Services, Georgetown University Hospital, 3800 Reservoir Rd. NW, Room 2419M, Washington, D.C. 20007. 625-7379.

* George Washington University Medical Center Travelers' Clinic, 2150 Pennsylvania Ave. NW, Washington, D.C. 20037. 676-8466.