Polyphenolic flavonoids are among a wide variety of phytochemicals present in the human diet. Basic research, animal model, and human studies suggest flavonoid intake may reduce the risk of several age-related chronic diseases. The vast number of flavonoids and mixtures of their subclasses, including flavonols, flavones, and flavanones, and the variety of agricultural practices that affect their concentration in foods have presented a challenge to the development of adequate food composition databases for these compounds. Nonetheless, dietary assessments have been applied to cohort and case-control epidemiological studies, and several reveal an inverse association with risk of some forms of cancer, cardiovascular disease, and other chronic conditions. Those observational studies that have examined these relationships with regard to flavonols, flavones, and flavanones are reviewed. The requirement for caution in interpreting these studies is discussed with regard to the limited information available on the bioavailability and biotransformation of these flavonoids. As the totality of the available evidence on these flavonoids suggests a role in the prevention of cancer and cardiovascular disease, further research is warranted, particularly in controlled clinical trials.