Objective: Functional hypothalamic amenorrhoea (FHA) is a common cause of amenorrhoea, but few non-specialist clinicians are able to diagnose affected women. The aim of this study was to investigate the clinical and biochemical features of FHA, compared to that of polycystic ovarian syndrome (PCOS) and assess the diagnostic performance of the different parameters for differentiating between the two conditions. Design: A retrospective observational study Setting: Specialist reproductive endocrine gynaecology clinic, St Mary’s Hospital, London, UK Population: Women diagnosed with FHA and PCOS following specialist assessment. Methods: Clinical and biochemical data were collected from electronic hospital data base. Results: Compared with PCOS, women with FHA had significantly lower body mass index (BMI) (20.1±2.9 vs 31.1±7.8 kg/m2, P<0.0001) and a thinner endometrium (3.75±2.23 vs 6.82±3.32 mm, P<0.0001). Women with FHA had significantly lower luteinising hormone (LH) (3.46±7.31 vs 8.79±4.98 IU/L, P< 0.0001), as well as lower LH: follicle stimulating hormone (FSH) ratio, estradiol, thyroid-stimulating, free thyroxine and prolactin levels; there was no significant difference in FSH levels. Low BMI had the greatest predictive performance for FHA (area under the curve [AUC]; 0.93, P<0.001), followed by low estradiol (AUC 0.89, P<0.001), low LH (AUC 0.88, P<0.001) and LH:FSH ratio (AUC 0.86, P<0.001). Conclusions: Our data provides quantification for diagnostic accuracy of clinical parameters to differentiate FHA from PCOS, namely low BMI, estradiol, LH and LH:FSH ratio. These data could help clinicians more reliably diagnose FHA in women with secondary amenorrhoea. Key words: Amenorrhoea, Hypogonadism, Polycystic Ovarian Syndrome, Luteinising Hormone