Aim Polycystic ovary syndrome (PCOS) is the most prevalent endocrine disorder in women and confers a substantial health burden. It is important to explore modifiable extrinsic factors that contribute to disease risk. The aim of the present study was to compare the dietary intake, physical activity and physiological characteristics of women with PCOS with those of controls to identify lifestyle behaviours associated with known cardiometabolic risk factors. Methods A seven-day food and activity diary was completed and anthropometric and biomarkers of type 2 diabetes mellitus and cardiovascular disease risk were measured in 38 women with PCOS, and 30 controls, matched for age and body mass index. Results Similar energy intakes and activity levels were observed between groups. Percentage energy intakes from total, saturated and monounsaturated fats were significantly higher (P = 0.008, P = 0.012 and P = 0.003, respectively) and % energy from carbohydrate was significantly lower (P < 0.001) in participants with PCOS compared with controls (P < 0.001). Insulin levels, two hours after a glucose challenge, were significantly higher in PCOS participants compared with controls (P = 0.029). Increased dietary glycaemic index appeared to be associated with a more negative biochemical profile in women with PCOS compared to controls, being significantly associated with an increased waist circumference and LDL-cholesterol and decreased HDL-cholesterol. Conclusions The present study has identified suboptimal dietary patterns in women with PCOS, and highlighted dietary factors associated with cardiometabolic risk factors that warrant monitoring in both lean and obese women with PCOS.