Cushing’s disease is a rare and often difficult diagnosis. Therefore, a significant delay between the onset of symptoms and the final diagnosis frequently occurs. We present a previously healthy twelve year old boy in whom hypercortisolism was suspected based on clinical symptoms: abrupt excessive weight gain in combination with growth arrest since 9 months, despite adequate exercise and dietary interventions. The results of conventional biochemical diagnostics for Cushing’s disease (late-night salivary cortisol, 24h urine free cortisol, low-dose dexamethasone suppression test, combined 48h dexamethasone-CRH test) were contradicting and could not confirm the diagnosis. Because of a persistent clinical suspicion after a wait-and-see period, cortisol levels in the boy’s 11 cm long hair were analyzed. The very high hair cortisol levels supported the clinically suspected Cushing’s disease. MRI of the pituitary showed evidence of an adenoma, which was confirmed postoperatively as an ACTH producing adenoma. This confirmed the diagnosis of Cushing’s disease, 1.5 years after the initial presentation. This case report emphasizes the added value of hair cortisol in a challenging diagnosis of Cushing’s disease.