Background Women with polycystic ovarian syndrome (PCOS) commonly consult endocrinologists or gynaecologists and it is not known whether these specialty groups differ in their approach to management.Objective To compare the investigation, diagnosis and treatment practices of endocrinologists and gynaecologists who treat PCOS.Design and Setting A mailed questionnaire containing a hypothetical patient's case history with varying presentations - oligomenorrhoea, hirsutism, infertility and obesity - was sent to Australian clinical endocrinologists and gynaecologists in teaching hospitals and private practice.Results Evaluable responses were obtained from 138 endocrinologists and 172 gynaecologists. The two specialty groups differed in their choice of essential diagnostic criteria and investigations. Endocrinologists regarded androgenization (81%) and menstrual irregularity (70%) as essential diagnostic criteria, whereas gynaecologists required polycystic ovaries (61%), androgenization (59%), menstrual irregularity (47%) and an elevated LH/FSH ratio (47%) (all P-values < 0.001). In investigation, gynaecologists were more likely to request ovarian ultrasound (91%vs. 44%, P < 0.001) and endocrinologists more likely to measure adrenal androgens (80%vs. 58%, P < 0.001) and lipids (67%vs. 34%, P < 0.001). Gynaecologists were less likely to assess glucose homeostasis but more likely to use a glucose tolerance test to do so. Diet and exercise were chosen by most respondents as first-line treatment for all presentations. However, endocrinologists were more likely to use insulin sensitizers, particularly metformin, for these indications. In particular, for infertility, endocrinologists favoured metformin treatment whereas gynaecologists recommended clomiphene.Conclusions There is a lack of consensus between endocrinologists and gynaecologists in the definition, diagnosis and treatment of PCOS. As a consequence, women may receive a different diagnosis or treatment depending on the type of specialist consulted.