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Dietary flavonoids exert bone-protective effects in animal models, but there is limited information on the effect of different flavonoid subclasses on bone health in humans. The aim of this observational study was to examine the association between habitual intake of flavonoid subclasses with bone mineral density (BMD) in a cohort of female twins. A total of 3160 women from the TwinsUK adult twin registry participated in the study. Habitual intakes of flavonoids and subclasses (flavanones, anthocyanins, flavan-3-ols, polymers, flavonols, and flavones) were calculated from semiquantitative food frequency questionnaires using an updated and extended U.S. Department of Agriculture (USDA) database. Bone density was measured using dual-energy X-ray absorptiometry. In multivariate analyses, total flavonoid intake was positively associated with higher BMD at the spine but not at the hip. For the subclasses, the magnitude of effect was greatest for anthocyanins, with a 0.034 g/cm2 (3.4%) and 0.029 g/cm2 (3.1%) higher BMD at the spine and hip, respectively, for women in the highest intake quintile compared to those in the lowest. Participants in the top quintile of flavone intake had a higher BMD at both sites; 0.021 g/cm2 (spine) and 0.026 g/cm2 (hip). At the spine, a greater intake of flavonols and polymers was associated with a higher BMD (0.021 and 0.024 g/cm2, respectively), whereas a higher flavanone intake was positively associated with hip BMD (0.008 g/cm2). In conclusion, total flavonoid intake was positively associated with BMD, with effects observed for anthocyanins and flavones at both the hip and spine, supporting a role for flavonoids present in plant-based foods on bone health. © 2012 American Society for Bone and Mineral Research.