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The aim of this study was to clarify the associations between menstrual cycle disorders, food frequency intake, dietary habits, and physical activity levels in women with and without Polycystic Ovary Syndrome (PCOS). 114 women with PCOS and 341 without PCOS (CONTROL) participated in the study. They were also divided into women with menstrual disorders(MD), and those with regular cycle (RC). Each of them completed a medical and Kompan questionnaires. In women with PCOS and menstrual disorders (PCOS-MD), intake of wholemeal products, meat and meat products, fats and alcoholic beverages was higher in comparison to those in the control group with menstrual disorders (CONTROL-MD). Women in the PCOS-MD group also reported significantly more frequent snacking between meals, higher Pro-Healthy Diet Index (pHDI-14), and a lower level of physical activity at leisure time than CONTROL-MD. Women with PCOS differed from those in CONTROL due to a higher consumption of meat and meat products, fats, fruits and vegetables, juices and alcoholic beverages, and a lower intake of whitemeal products, sweets, and fruits. Women with PCOS more frequently snacked, but the number of their meals was also lower. In women with PCOS, menstrual disorders may be related not only with diet quality and physical activity but also with snacking and skipping meals.