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Although most things in autoimmune diseases are very poorly understood now and there is very little known about how they work, hormones in general have a connection to autoimmune diseases. Pregnancy also has quite a bit to do with autoimmune diseases usually by increasing your risk of getting an autoimmune disease if you've had one in the past year. On the other hand some women have the opposite effect by protecting a woman with an autoimmune disease. So essentially it is unsure what the reason is pregnancy and hormones play a part. (sources: Living well with Autoimmune Disease)

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