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Foods that have a high fat content in general may cause heartburn/reflux so perhaps as the fish oil pills are being digested it's causing the same problem. Some fish oil pills have a nasty side effect of you burping up a fishy taste and it helps if you keep your fish oil pills in the freezer to reduce this side effect. Perhaps try putting them in the freezer to see if that reduces heartburn as well.

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Q: Do fish oil pills cause heartburn?
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