(FORTUNE Magazine) – Like almost everyone, Naomi Solo, 62, dreads a colonoscopy. The procedure--the most effective way to screen for colon cancer and growths, called polyps, from which it can develop--involves a day of fasting and bowel cleansing, then sedation and an exam of the colon using a five-foot-long probe. Solo had a colonoscopy in 1978 while being treated for an intestinal illness. Her doctors recommended follow-up screenings, she says, but "I never went back because I found the whole thing so traumatic."

Squeamishness about colonoscopies helps explain why colon cancer is so deadly (the only malignancy that kills more people is lung cancer). Beyond eating a healthy diet, avoiding tobacco, and exercising regularly, the best way to prevent it is regular screening. But since most screening methods involve collecting a stool sample or taking laxatives and having a tube inserted up your rear, only one-third of people over 50--the age at which doctors recommend testing for those without a family history of colorectal cancer--have any kind of screening. That's tragic, because if precancerous growths are removed early, 70% to 90% of colon cancer can be avoided; just half the people who seek treatment after symptoms appear will survive at least five years.

The most commonly used screens for colon cancer are the fecal occult blood test (FOBT), which tests the feces for evidence of intestinal bleeding, and flexible sigmoidoscopy, which uses a scope to examine the lower third of the colon. Doctors typically recommend an FOBT annually and a sigmoidoscopy every five years. However, recent studies have shown that neither method is nearly as effective as a colonoscopy, which examines the whole colon. But besides being, well, gross, a colonoscopy costs between $1,000 and $2,000--and is not covered by many insurers.

An experimental procedure called virtual colonoscopy may offer a better solution. It uses a CT scan to take hundreds of radiographic slices of the abdomen. Software cobbles together these slices, enabling a radiologist to "fly through" the colon on a computer screen. The view closely resembles what a doctor would see in a standard colonoscopy. The virtual version does entail bowel cleansing, but doctors prescribe milder laxatives than those for the standard procedure. And although virtual colonoscopy is still somewhat invasive--a tube must be inserted an inch or two into the rectum to fill the colon with air--it takes just 15 minutes, vs. 30 to 60 minutes, plus a few hours of recovery from anesthetic, for a standard colonoscopy.

Studies suggest that the procedure, which costs between $500 and $1,000, may be as effective as conventional colonoscopy in finding cancers and large polyps. But there are tradeoffs. If polyps are found--as they are in 10% of people who have a virtual colonoscopy--a standard colonoscopy is needed to remove them. Nor are virtual colonoscopies universally available. Most are performed at teaching hospitals such as those at New York University, Mass General in Boston, Washington University in St. Louis, and the University of California at San Francisco.

The future of colon-cancer screening may lie in totally noninvasive molecular tests that would replace the FOBT. One, by EXACT Sciences in Maynard, Mass., works by examining fecal matter for abnormal DNA that cancer cells and precancerous growths shed into the colon. The test has been 91% effective in detecting cancers in trials at the Mayo Clinic; while not expected to entirely eliminate the need for colonoscopy, it could be widely available within three years. A blood test being developed by Amplistar, in Winston-Salem, N.C., works by identifying antibodies specific to colon cancer. If it proves effective, it may be available within five years.

--JEREMY KAHN