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A growing body of evidence highlights the properties of flavonoids in natural foods for disease prevention. Due to their antioxidative, anti-inflammatory, and anti-carcinogenic activities, flavonoids have been revealed to benefit skeletal muscle, liver, pancreas, adipocytes, and neural cells. In this review, we introduced the basic classification, natural sources, and biochemical properties of flavonoids, then summarize the experimental results and underlying molecular mechanisms concerning the effects of flavonoid consumption on obesity, cancers, and neurogenerative diseases that greatly threaten public health. Especially, the dosage and duration of flavonoids intervening in these diseases are discussed, which might guide healthy dietary habits for people of different physical status.