Cutting an onion makes you cry because, once it is cut, a dedicated enzyme turns its sulfur compounds into a tear-inducing molecule. The chapter on why cutting onions makes you cry walks through that chain of reactions. Onion also carries something with two faces: its fructans feed gut bacteria, and they also make people with irritable bowel syndrome () bloated.
Onion (Allium cepa) is in the same allium family as garlic and is also a bulb made of wrapped layers. It is one of the most-eaten vegetables in the world, often not the star of a dish but the thing that sets its base flavor.
It is among the richest dietary sources of flavonoids, especially quercetin, while claims such as "a cut onion absorbs germs and prevents flu" have no basis.
Background · A flavor base with two sides
Onion is the flavor base of nearly every cuisine: from Chinese stir-fries to French onion soup, it is often not the star but sets a dish's underlying taste. Because it is so ordinary, both of its sides tend to be overlooked:
One side is real nutrition: it is among the richest dietary sources of flavonoids and also carries a good amount of prebiotic fiber, the kind that feeds beneficial gut bacteriaThe other side is a real nuisance plus a real myth: cutting it makes you cry through a precise enzyme mechanism; it is one of the most common trigger foods for people with ; and the folk belief that it soaks up germs is simply false This story covers four things: why it makes you cry, its real nutritional value, why the same substance "feeds the gut" for some people and "causes bloating" for others, and which claims to drop. Together with its close relative garlic, it makes a matching pair: in both, the signature is an enzyme that switches on only once the bulb is cut.
Chapter 2
Why cutting onions makes you cry
Crying over an onion is not a vague matter of onions being irritating. Behind it is a precise chain of enzyme reactions, and the key step was worked out only in 2002.
In an intact onion, the sulfur-containing raw material and the enzymes are stored apart, so it barely stings. Once you cut it, a first enzyme turns the raw material into an intermediate, and a second, dedicated enzyme turns that into the tear-inducing molecule that drifts into your eyes. Chilling the onion before cutting, using a sharp knife, and cooking it are all ways of working against those two enzymes.
A CLOSER LOOK
A second enzyme makes the tear factor
Follow the arrows through the two reaction steps; molecular symbols are schematic, and the tear factor then travels to the eyes.
1Alliinase acts first
After cells are cut, alliinase converts the sulfur precursor to an intermediate.
2LFS adds the next step
The separate lachrymatory-factor synthase converts the intermediate into the volatile tear factor.
Illustration for understanding; not to scale. Saved figures include explanations and sources.
Mechanism · A second enzyme makes the tear factor
In an intact onion, the sulfur-containing precursors and the enzymes are stored apart, so there is almost no sting. Once you cut it, cells burst and alliinase first converts a sulfur precursor into an intermediate.
For a long time, the tear-causing substance was thought to be just a natural byproduct of that reaction. But a study published in Nature in 2002 found that the tear factor is actually made by a separate enzyme, lachrymatory-factor synthase (LFS) (Imai 2002). It specifically converts the intermediate into volatile (Z)-propanethial S-oxide, the small molecule that drifts into your eyes, irritates the nerves of the cornea, and sets off the tear reflex.
The discovery also explains how tearless onions could later be bred: stop LFS from working, and the sulfur flavor compounds still form, but the tear factor no longer does.
Practical countermeasures (each one goes back to the mechanism)
Chill it before cutting: cold slows the enzymes and reduces evaporationUse a sharp knife: clean cuts break fewer cells, so less enzyme is releasedVentilate, lean back, or cut near running water: the volatile molecule is carried away or dissolves in the waterCut the root end last: a common explanation is that the enzymes are most concentrated in the root plateCooked onion brings no tears: heat inactivates the enzymes, so cooked onion does not sting the eyes and tastes sweeter (the sulfur compounds break down and the sugars come through)
Chapter 3
Quercetin, mostly in the outer layers
The most underrated thing about onion nutritionally is that it is among the richest dietary sources of flavonoids, led by quercetin, and the quercetin is concentrated in the outer layers, so peeling too much throws away the most valuable part.
But one line has to be drawn clearly: eating onions is not the same as taking a quercetin supplement. Quercetin's antioxidant and anti-inflammatory activity in experiments does not mean that eating it prevents disease, and the antiviral and immune-boosting claims made for high-dose capsules mostly lack reliable human evidence.
Numbers · Outer layers hold it; capsules are different
Yellow onions contain about 270-1187 mg/kg of flavonols, and red onions more (415-1917 mg/kg; the red color comes from additional anthocyanins) (Slimestad 2007, J Agric Food Chem). Quercetin is concentrated in the outer layers and just under the skin: you do not eat the papery outermost skin, but the few layers right beneath it are the most valuable.
Quercetin is a plant flavonoid that, in experiments, shows antioxidant and anti-inflammatory activity and stabilizes mast cells (immune cells involved in allergy). In observational studies, people who eat more flavonoids have a lower risk of cardiovascular disease, but this is an association.
A few boundaries:
1. Quercetin in food and quercetin in capsules are different things: in food it comes as glycosides that are absorbed after cooking and processing in the gut, at modest doses; the antiviral, immune-boosting, and anti-cancer claims for high-dose quercetin capsules mostly lack reliable human evidence. 2. Activity in a mechanism is not a clinical benefit: being an antioxidant in a cell does not mean preventing disease when eaten. This is the step nutrition most often skips, the same point the Garlic story makes about the lab dish and the body. 3. Simply treat onion as a good everyday source of flavonoids: its value is in supplying these plant compounds over the long term, with meals, at low cost, not in some magic dose.
Also, allium sulfur compounds together with flavonoids are thought to be a possible basis for the observation that people who eat a lot of onions and garlic have a lower risk of cardiovascular disease and some cancers, but that is still correlation, not causation.
Chapter 4
One fiber feeds microbes and bloats
Onion carries a mechanism that is both elegant and contradictory: what makes it good for the gut and what makes some people painfully bloated are the same molecules, called fructans.
The small intestine cannot digest fructans, so they reach the large intestine intact and are fermented by bacteria. For most people that makes them a prebiotic that feeds beneficial bacteria; for people with irritable bowel syndrome (), the gas from fermentation and the water drawn into the gut bring bloating and pain. Onion is one of the most common high- foods (FODMAPs are short-chain carbohydrates that are poorly absorbed and fermented by bacteria). Whether that is good or bad depends not on the onion but on your gut.
Mechanism · Feeds microbes or bloats, depending on the gut
Onion is rich in fructans (soluble fibers such as fructo-oligosaccharides and inulin). The human small intestine cannot digest them, so they reach the large intestine intact and are fermented by beneficial bacteria such as Bifidobacteria, producing short-chain fatty acids () that feed the gut microbiome and support the gut barrier. That is exactly what a prebiotic is (see Gut microbiome). For most people this is onion's hidden health bonus.
But for people with irritable bowel syndrome (), or anyone who bloats easily, the same not-absorbed, fermented-in-the-colon route means gas, plus water pulled into the gut by osmosis, which adds up to bloating, rumbling, pain, and changes in bowel habits. Onion is recognized as one of the highest- foods (the F stands for "fermentable", and fructans belong there).
The evidence (Halmos 2014, Gastroenterology): in a randomized crossover controlled trial, a low-FODMAP diet reduced overall IBS symptoms more than a typical Australian diet did. Onion and garlic are high in fructans, so low-FODMAP menus usually drop them first; but that is menu design, not a ranking of foods published by this trial.
How to reconcile the two
Fructans dissolve in water, not in oil: onion or garlic oil (fry the pieces in oil, then lift them out) keeps the flavor while leaving most of the FODMAPs in the solids, a practical trick for people with IBS (the same works for garlic)Green tops are not the same as white bulbs: the green part of scallions and spring onions is low in FODMAPs and can stand in for flavorLow-FODMAP does not mean never eating it again: you remove it first, then test your own tolerance step by step through the three phases described in the Irritable Bowel Syndrome story For a healthy gut, onion is a prebiotic bonus; for a sensitive gut, it is a trigger. The onion is neither good nor bad; it depends on your gut.
Chapter 5
Can a cut onion prevent flu?
The most widespread folk claim about onions is that leaving a cut onion in the room absorbs germs from the air and prevents flu.
Bacteria and viruses are not drawn into an onion; there is no physical or biological mechanism by which it could pull pathogens out of the air like a magnet. Flu spreads through droplets and contact, and an onion sitting on a table does nothing to change that chain.
Myth · Ask how it works and these claims fall apart
The idea that "a cut onion prevents flu" has never been supported by any controlled study, and the US National Onion Association, among others, has specifically debunked it.
A related claim, that "a cut onion left out turns toxic or soaks up so many bacteria it is unsafe", is also exaggerated. A cut onion, like any cut vegetable, grows bacteria over time, should be refrigerated, and should not be kept long; but that is ordinary food-safety sense, not a special onion toxicity.
Some say that putting onions in your socks will draw out toxins and that eating raw onion will clear your arteries; these claims have no evidence either: an onion against the sole of your foot does not detox you, and eating raw onion does not dissolve blood clots.
How to spot this kind of myth: they all skip the mechanism, offering a scary or tempting conclusion without explaining how an onion could possibly do it. The moment you ask "what is the mechanism, and is there evidence in people?", these claims fall apart. That is exactly the kind of judgment worth practicing.
The onion's real value (flavonoids and prebiotics) is good enough already; it does not need these myths to prop it up.
Chapter 6
Storing, cutting, and cautions
Whole onions keep for weeks in a cool, dry place; once cut, seal them, refrigerate them, and use them within a few days.
Who should pay attention: people with irritable bowel syndrome () should drop onion first and use scallion greens or onion oil for flavor instead; for people with acid reflux, raw onion is a common trigger; and because quercetin is concentrated in the outer layers, do not peel too much away.
In practice · Choosing, storing, cutting, and who holds off
Choosing and storing: pick onions that are firm, with dry skins and no sprouts or soft spots. A common tip is not to store them with potatoes, on the grounds that each speeds the other's spoilage.
Cutting without tears: chill before cutting, use a sharp knife, keep the air moving, and cut the root end last. Once cooked, onion no longer brings tears and tastes sweeter.
Keeping the nutrients: quercetin is concentrated in the outer layers, so do not over-peel; letting cut onion rest briefly helps flavor compounds form (the same as with garlic). Raw onion is sharp and keeps more of its flavonoids; cooked onion is milder and easier to digest.
How much: as an everyday vegetable and seasoning, there is no amount you need to make a point of eating. Treat it as a flavor base plus a source of flavonoids and prebiotics, eaten with meals.
Who should pay attention
Irritable bowel syndrome () or bloating easily (the key group): onion is a classic high- food; during flare-ups drop it first, use scallion greens or onion oil for flavor, and then test your tolerance through the three phases described in the Irritable Bowel Syndrome storyGastroesophageal reflux disease (): raw onion is a common reflux trigger, so sensitive people should take note (see GERD)Taking blood thinners or antiplatelet drugs, or facing surgery: alliums in large amounts may slightly affect clotting; people taking high-dose supplements (not ordinary food amounts) should ask a doctor firstStarting solids for babies: small amounts of cooked onion are usually well tolerated This page provides general information only and does not replace a doctor's judgment about your health.
References · 5
U.S. Department of Agriculture, Agricultural Research Service. (2024). FoodData Central: Onions, raw (SR Legacy). Composition reference for raw onion. fdc.nal.usda.gov/food-search?query=onions%20raw
Imai, S., Tsuge, N., Tomotake, M., Nagatome, Y., Sawada, H., Nagata, T., & Kumagai, H. (2002). An onion enzyme that makes the eyes water. Nature, 419(6908), 685. Showed the onion lachrymatory factor ((Z)-propanethial S-oxide) is produced by a dedicated enzyme, lachrymatory-factor synthase (LFS), not merely as a byproduct of alliinase. 10.1038/419685a
Slimestad, R., Fossen, T., & Vågen, I. M. (2007). Onions: a source of unique dietary flavonoids. Journal of Agricultural and Food Chemistry, 55(25), 10067-10080. Onions are among the richest dietary flavonoid sources; quercetin derivatives dominate (yellow onions ~270-1187 mg/kg, red ~415-1917 mg/kg flavonols). 10.1021/jf0712503
Halmos, E. P., Power, V. A., Shepherd, S. J., Gibson, P. R., & Muir, J. G. (2014). A diet low in FODMAPs reduces symptoms of irritable bowel syndrome. Gastroenterology, 146(1), 67-75. Randomized controlled cross-over trial; a low-FODMAP diet significantly reduced overall IBS symptoms versus a typical Australian diet. Onion and garlic are among the highest-fructan (FODMAP) foods. 10.1053/j.gastro.2013.09.046