Oral levothyroxine treatment appears to be easy to manage but the hormone absorption can be impaired by several interfering factors, leading to abnormal TSH levels. Therefore, patients can be at risk of both under and over treatment. A 41 years old woman came to our attention for Hashimoto's thyroiditis with refractory hypothyroidism and a malabsorption has been suspected. The patient entered a diagnostic work up which revealed the unusual cause of malabsorption. The patient underwent specific treatment for the disorder with a progressive improvement of the levothyroxine absorption.