This cross-sectional study aimed to examine the association between different body composition measures, menstrual cycle characteristics, and hormonal factors in a population-based sample of young women. The study sample included 726 Australian women aged 26-36 years who were not currently taking hormonal contraceptives and were not currently pregnant or breast feeding. Anthropometric measures included BMI, waist circumference (WC), and waist-hip ratio (WHR). Menstrual cycle characteristics were self-reported and usual cycles defined as short (<or=25 days), normal (26-34 days), or long (>or=35 days). Cycles were defined as irregular if there were >or=15 days between the longest and shortest cycle in the past 12 months. Fasting serum levels of sex hormone-binding globulin (SHBG), testosterone, insulin, and glucose were measured and the free androgen index (FAI) derived. Compared with those of normal weight, obese women had at least a twofold greater odds of having an irregular cycle, whether defined by BMI (odds ratio (OR) = 2.61; 95% CI = 1.28-5.35), WC (OR 2.28; 95% CI = 1.16-4.49), or WHR (OR = 2.27; 95% CI = 1.09-4.72). Body composition measures were significantly positively associated with fasting insulin, testosterone, and FAI, and negatively associated with SHBG (P < 0.01). Fasting insulin, SHBG, and FAI had the strongest influence on the associations between obesity and irregular cycles, with statistically significant ORs of having an irregular cycle being attenuated to near null values following adjustment. In conclusion, both overall and central obesity were significantly associated with having an irregular menstrual cycle. This association was substantially influenced by hormonal factors, particularly insulin and SHBG.