Objective Clinical data on primary hypophysitis are still scarce. Especially non-surgical cases are underreported. We sought to analyse clinical characteristics of primary hypophysitis, particularly in clinically diagnosed patients. Design Retrospective single centre study in 60 patients with primary hypophysitis. Methods Symptoms, MRI, histopathological findings, treatment and outcomes were analysed in 12 histopathologically and 48 clinically diagnosed patients. Diagnostic criteria for clinical diagnosis were: a) MRI findings compatible with primary hypophysitis; b) course of disease excluding other differential diagnoses. Mean duration of follow-up was 69 months. Results Female sex was predominant (73%). Fatigue (52%), headache (38%) and diabetes insipidus (38%) were the most frequent symptoms. 42% had a concomitant autoimmune disease. The corticotropic, thyrotropic, gonadotropic, somatotropic axis was impaired in 67%, 57%, 52%, 20%, respectively. Men had a higher number of impaired hormone axes (p=0.022) with the gonadotropic axis being affected more frequently in men (p=0.001). Infundibular thickening (56%) and space occupying lesions (46%) were typical MRI findings. Pituitary size was frequently enlarged at presentation (37%) but diminished during observation (p=0.029). Histopathologically and clinically diagnosed cases did not differ. Conclusions The cohort of clinically diagnosed patients did not differ from our histopathologically diagnosed patients or from published cohorts with predominantly surgical patients. Thus, diagnosis of primary hypophysitis using clinical criteria seems feasible.