What happens if I finish my last two days of Clomid (clomiphene) with 50mg instead of 100mg, cause of side effects?

No big difference. It will probably make little difference to your treatment. Discuss the side effects with your md to make sure that they are really associated with the clomid (clomiphene). Letrozole (femara) may be an alternative for your next treatment cycle. If you are doing a Clomid (clomiphene) challenge test (also known as a cct or ccct) it is better to stick to the 100 mg dose for the full five days. Best wishes.