Lymphocytic or granulomatous hypophysitis is a rare entity with a difficult diagnosis. Our objective was to report a patient with non-tuberculous granulomatous hypophysitis. An HIV-negative 45-year old man with confusional state, subacute ophthalmoplegia, and clinical and laboratory findings of panhypopituitarism was seen in the emergency unit. A cranial MRI showed a sellar mass suggestive of hypophysitis. After an unsuccessful attempt with steroids and antituberculous drugs the patient died. Post-mortem histopathology revealed granulomatous lesions and restriction fragment length polymorphism analysis confirmed the presence of Mycobacterium gordonae’s DNA. In conclusion, we should consider granulomatous hypophysitis in the differential diagnosis of non-secreting hypophyseal tumors. The etiology of a pituitary granuloma by a non-tuberculous mycobacteria is best reached by histopathological techniques and molecular assays. The optimal therapy is yet to be established.