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Plant diseases
Neck rot
Botrytis allii and Botrytis aclada · Fungus
Also called onion neck rot (UK), Botrytis neck rot (USA).
Illustration
A grey mould that rots stored onions from the neck down, several weeks to a couple of months after harvest. It gets in while they grow or as they are lifted, so avoid late feeding, harvest on a dry day, dry the necks hard before storing, and keep onions cool, dry and airy.
How to spot it
- Onions that looked healthy at harvest soften at the neck after several weeks to two months in store.
- The neck looks water-soaked or sunken, and the scales turn soft and brown, as if cooked, from the neck downwards.
- Dusty grey mould between the scales and around the neck.
- Later, hard black crusts or lumps, up to 1.5 cm (⅝ in) across, around the neck and under the scales.
- In the end the bulb dries out, shrunken and mummified.
Easily confused with
White rot
Strikes growing plants in the ground, with white, fluffy mould and poppy-seed black dots on the base of the bulb.
Black mould
Sooty black powder under the dry outer skins, worst after hot weather and in warm storage.
Bacterial soft rot
A watery, strong-smelling rot with no grey mould; the inner scales may slide out when the bulb is squeezed.
Where it's a problem
- Worldwide: A common storage problem wherever onions are grown, worst after dull, wet summers and wet harvests. A bad outbreak can spoil more than half of a stored crop.
What to do
- Buy seed and sets from a reputable supplier; some seed companies treat their seed against it.
- Don't overfeed with nitrogen, and give no feed once the bulbs start to swell: late feeding delays ripening.
- Stop watering as the bulbs ripen, and let the tops yellow and fall before lifting.
- Lift on a dry day and handle the bulbs gently: bruises and cuts let it in.
- Dry the bulbs in the sun or an airy shed until the necks are dry and tight before you trim the tops: the fungus can't grow through dry tissue.
- Use thick-necked, bruised or soft onions first. Store only firm, dry ones somewhere cool, dry and airy, and check them every few weeks.
- Keep onions out of a bed where neck rot has been for three years.
In the UK there are no fungicides for gardeners against it, and in Australia none is registered for treating stored onions. Good drying and storage are the fix.
Follow your local council's guidance for disposing of diseased plant material.
Vegetables it affects
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Sources
- RHS: Onion neck rot
- UMass Extension: Alliums, Botrytis neck rot
- Utah State University Extension: Botrytis neck rot
- Agriculture Victoria: Onion storage diseases
- Texas A&M Plant Disease Handbook: Onion
Facts checked Wednesday 21 October 2026. General guidance only: follow your local council, agency and product label.