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The Well Column Tara Parker-Pope on living well.

Neti pots — those odd teapotlike vessels used to wash out the nasal passage — have won legions of fans who rely on them for relief from allergies, congestion and colds.

But now, after two cases of a deadly brain infection were linked to neti pots, government health officials have issued new warnings about using them safely.

The Food and Drug Administration last month reported on two cases in Louisiana in which patients contracted infections after using neti pots filled with tap water. The culprit was an amoeba called Naegleria fowleri, which is commonly found in lakes, rivers and hot springs.

This kind of infection is exceedingly rare, but it usually occurs when people get water up the nose after swimming or diving in lakes or rivers; Naegleria fowleri can travel from the nose into the brain, where it causes primary amoebic meningoencephalitis, a disease that destroys brain tissue and is almost always fatal. In 123 known cases from 1962 to 2011 in the United States, only one person has survived, according to the Centers for Disease Control and Prevention.

Last year, Louisiana state health officials reported on two unrelated deaths — of a 20-year-old man and a 51-year-old woman who were believed to have been infected by tap water later found to be contaminated with Naegleria fowleri. Both had used tap water in a neti pot. (Because stomach acid kills the amoeba, drinking contaminated water does not lead to infection.)

As a result, the F.D.A. has issued new warnings reminding consumers to use distilled or filtered water in a neti pot. They can use bottled water, or they can boil water and let it cool before using.

Doctors say the new warnings should not dissuade people from using a neti pot, which can be a safe and effective home remedy for allergies and congestion.

To use a neti pot, a person mixes water with a saline packet to create a mild saline solution. Leaning over a sink, the user inserts the spout of the pot into a nostril, allowing the water to wash up inside the nasal passage and flow out the other nostril. Nasal lavage bottles can also be used, although it is important not to squeeze the bottle too hard.

“Initially it’s a weird sensation, but if you’re congested and it washes out some of that stuff, you’re much less miserable,” said Dr. Rohit K. Katial, a professor of medicine and allergy specialist at National Jewish Health, a respiratory hospital based in Denver. “People end up really liking it because they feel refreshed — it’s wellness with water.”

Several studies show that regular nasal irrigation can reduce symptoms of allergies and congestion. One 2008 study found that children with severe allergies were less reliant on steroid nasal sprays if they regularly rinsed their nasal passages.

“One of the primary functions of the nose is filtration,” Dr. Katial said. “That’s where you capture all the pollens and particulates. Irrigation is the way to wash some of that out, and we think it’s very beneficial and we use it fairly extensively in our patients.”

Doctors say it’s important to keep the risk of Naegleria fowleri contamination in perspective. Most cases are in the South, although some have been documented in the Midwest and as far north as Minnesota. Millions of people swim and dive in lakes and rivers each year, yet from 2002 to 2011 there were only 32 reported Naegleria fowleri infections, according to the disease centers. By comparison, from 1996 to 2005, the most recent period with available data, the United States had more than 36,000 drowning deaths.

With neti pots and other forms of nasal lavage, the greater risk comes from improper cleaning. Bacteria or fungi can form on the spout of a used neti pot or in a partly used nasal lavage bottle. Regular use of an improperly cleaned neti pot or contaminated lavage bottle can lead to chronic irritation or allergies.

And like toothbrushes, neti pots shouldn’t be shared with anyone. People with a compromised immune system should consult a doctor before using a neti pot.

While the two recent cases of amoebic infection may be terrifying, the public should not be alarmed or fearful about freshwater swimming or neti pot use, said Dr. Philip T. Hagen, vice chairman of the Mayo Clinic’s division of preventive medicine.

“If you talk about the general population, there are more common things to be aware of and worry about than a scary amoebic infection,” said Dr. Hagen, who is also the editor of “The Mayo Clinic Book of Home Remedies.” “It’s an opportunity to remind people to be cautious and use good cleaning approaches and maintenance of their neti pot.”