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Most people can eat shallots and other onions without any side effects, although for some they might be hard to digest or cause interactions with certain medications. Higher intakes of onions may worsen existing heartburn or acid reflux, for example, although they don’t usually cause heartburn in people who do not already have it.
Onions and shallots are also foods that can worsen IBS-related symptoms for some people, since they contain FODMAP carbohydrates that have the potential to cause digestive issues when they aren’t properly broken down in the gut. If you have IBS and related symptoms like constipation or bloating frequently, it’s worth doing an elimination diet and seeing if removing common-culprit foods like garlic and onions can help.
There have also been a small number of reports of allergies to onions, including among people with asthma, skin rashes and red, itchy eyes. Onions and shallots are safe for children and during pregnancy or nursing, but again they have the potential to add to acid reflux, which is something you’ll want to monitor. *
