In this case report we describe a 49 year-old man who presented with chronic urticaria, angioedema and soft stool consistency. During diagnostic examinations Hashimoto's thyroiditis was found even though the patient never had clear symptoms of this disease. Blastocystis hominis was isolated through a stool microbiologic examination, implicating that this parasite can cause the development of Hashimoto's thyroiditis and chronic urticaria. After two-weeks treatment with metronidazole the Blastocystis hominis was eradicated, then urticaria and angioedema disappeared. During the four years of follow-up, the patient presented without any symptoms, whereas thyroid hormones were normalized and anti-thyroid antibodies declined. For the first time in the literature we show that eradication of Blastocystis hominis can prevent the development of both symptomatic Hashimoto's thyroiditis and chronic urticaria.