In a short girl with celiac disease and Hashimoto's thyroiditis (HT), suspicion of an associated pituitary lesion was suggested by the finding of a thyroid function pattern that was not compatible with HT-related hypothyroidism (low FT4 with normal TSH). This case report reinforces the view that the finding of a normal TSH in presence of a low FT4 should always alert pediatricians and raise suspicion of central hypothyroidism, even when a primary thyroid disease has been already identified. In this case TSH deficiency played a critical role in disclosing diagnosis of craniopharyngioma (CP). Therefore, the subsequent work-up was directed towards investigating pituitary function and morphology. Endocrinological investigations evidenced a picture of TSH and other pituitary hormone deficiency, whereas magnetic resonance imaging revealed an intrasellar CP. Therefore, in this case TSH deficiency played a key-role in disclosing CP diagnosis.