My main side effect was because they had me on too high of a dose at first: I had severe abdominal cramping to the point of needing to go to the ER and needing a muscle relaxant (bellatal - sp?). My endocrinologist said that was not possible, but the second he put me on the right dose, it went away. Many people have idiosyncratic (personal to them and abnormal) reactions to medicines.
All I can say is that some experts believe that the synthetic hormones can give false results on the blood tests, making everything look fine, so I have opted for real thyroid hormone and take Armour Thyroid. My thyroid problem symptoms all completely went away within 6 months (many by 2 months) after starting the Armour Thyroid. I spoke with at least a hundred women online before switching who all had the same experience: doing much better on Armour Thyroid. Some doctors are hesitant to prescribe it because there is some bad press in the AMA that some doctor's buy into about it, but it's all misrepresented and untrue.