Most safety studies that have implications for genistein involved mixed isoflavones from soy or red clover. For more information, see the Safety Issues section of the Isoflavone article.
Regarding genistein alone, one large study reported that genistein caused significant gastrointestinal side effects in almost 20% of participants. 1
Additionally, some evidence suggests that the genistein in particular might impair immunity. One study in mice found that injected genistein has negative effects on the thymus gland (an organ that is important for immunity) and also causes changes in the prevalence of various white blood cells consistent with impaired immunity. 2 Although the genistein was injected rather than administered orally, the blood levels of genistein that these injections produced were not excessively high; they were comparable to (or even lower than) what occurs in children fed soy milk formula. In addition, there are several reports of impaired immune responses in infants fed soy formula. 3 4 5 While it is too early to conclude that genistein impairs immunity, these findings are a potential cause for concern.
To read about more studies (and side effects within those studies), visit the Overview of Genistein.