Isoflavones are naturally occurring flavonoids characterized by a structure able to exert non-steroidal estrogen-like activity on human cells. The atypical linkage between the rings B and C remarkable influences these potentialities and confers them specific applications, along with the biochemical modification such as acetylation and malonylation. Plants belonging to Leguminosae family are the most abundant and rich sources for human organism, where, after their ingestion and metabolization, they show positive health effects on several diseases, especially in the prevention of coronary heart and neurological diseases, hormone-related cancers, osteoporosis, and postmenopausal symptoms. Although these molecules have been the subjects of numerous researches, their role for the wellness of the human organism remains controversial, due to the estrogen-like effects that can be a risk to certain individuals, especially, for instance, women with breast cancer or with the possibility to contract it. Moreover, there are substantial inconsistencies between the results obtained by epidemiologic studies conducted on Eastern population, which found high health promoting properties, and Western clinical trials, which found much less positive effects. In this review, we have performed a critical evaluation of available literature as far as isoflavones health promoting properties, risk assessment and mechanisms of action are of concern. In addition, we supply useful information on its biochemical properties, sources and bioavailability.