Abstract Study question Is the severity of menstrual dysfunction related to cardiometabolic risk markers in women with polycystic ovary syndrome (PCOS)? Summary answer PCOS women with amenorrhea, compared to those with oligomenorrhea or eumenorrhea, show a higher prevalence of insulin resistance (IR), prediabetes and hypertriglyceridemia. What is known already PCOS is associated robustly with a wide range of unfavorable cardiometabolic risk markers, including obesity, glucolipid metabolism disorders and metabolic syndrome. Many epidemiological studies have found compared to the women with regular menstrual cycles, women with a history of irregular menstruation increased the risks of metabolic syndrome and coronary heart disease. Recently, the association between the severity of menstrual cyclicity and hyperinsulinemia and IR has been demonstrated, suggesting menstrual history could be a simple but clinically important marker of metabolic dysfunction risk. But evidence linking the severity of menstrual cyclicity with cardiometabolic risk in PCOS women is very limited. Study design, size, duration In this prospective cross-sectional study, one hundred and fifty-four women diagnosed with PCOS by the Rotterdam criteria were recruited from July 2021 to September 2022. The association of menstrual cycle regularity with cardiometabolic risk markers including obesity, hypertension, glycemic abnormalities, dyslipidemia and metabolic syndrome was systematically analyzed. Participants/materials, setting, methods In a university-affiliated hospital, PCOS participants with eumenorrheic (Eumeno, n = 24), oligomenorrhea (Oligo, n = 73) and amenorrhea (Ameno, n = 57) underwent history and physical examination, gonadal steroid hormone measurement, lipid profile, oral glucose tolerance test (OGTT) and homeostasis model assessment of IR. Main results and the role of chance Adjusting for age, BMI and waist circumference, a trend toward an increase of unfavorable cardiometabolic risk markers including obesity, hypertension, prevalence of IR, prediabetes, hypertriglyceridemia and prevalence of metabolic syndrome was observed in Ameno group than in other menstrual categories. A significantly higher prevalence of IR, prediabetes and hypertriglyceridemia was demonstrated in Ameno group compared to the Eumeno or Oligo group. In logistic regression, adjusting for age, BMI, and waist circumference, Ameno women were more likely to have: IR than Eumeno women (odds ratio [OR]: 2.90; 95% CI: 1.01 to 8.31); prediabetes than Eumeno women (OR: 4.06; 95% CI: 1.05 to 15.77) and hypertriglyceridemia than Oligo women (OR: 4.43; 95% CI: 1.74 to 11.26). Moreover, the prevalence of IR, prediabetes and hypertriglyceridemia was still significantly higher in Ameno group than that in the Oligo or Eumeno group when further adjusted for free androgen index in the logistic regression. The proportion of Type 2 Diabetes, high total cholesterol, high low-density lipoprotein (LDL) cholesterol and low high-density lipoprotein (HDL) cholesterol was similar across the three groups. Limitations, reasons for caution Our study was limited by its cross-sectional nature, and another limitation was the cycle regularity question relied on the participant’s interpretation of irregular, although we have acquired the detailed menstrual cycle history and further reviewed at consultation, yet some exposure misclassification might also be present. Wider implications of the findings Our study used menstrual cycle as a readily obtainable marker for identification of PCOS women at greatest risk of IR, prediabetes and hypertriglyceridemia, which would emphasize the importance of menstrual cycle regularity and help refine the current recommendations concerning the screening of PCOS subjects for cardiometabolic diesases. Trial registration number 20210728