Genetic modification of plants has become common practice. However, root-specific genetic modifications have only recently been advocated. Here, a review is presented regarding how root-specific modifications can have both plant internal and rhizosphere-mediated effects on aboveground plant properties and plant performance. Plant internal effects refer to pleiotropic processes such as transportation of the modified gene product. Rhizosphere-mediated effects refer to altered plant–rhizosphere interactions, which subsequently feed back to the plant. Such plant–soil feedback mechanisms have been demonstrated both in natural systems and in crops. Here how plant internal and rhizosphere-mediated effects could enhance or counteract improvements in plant properties for which the genetic modification was intended is discussed. A literature survey revealed that rice is the most commonly studied crop species in the context of root-specific transgenesis, predominantly in relation to stress tolerance. Phytoremediation, a process in which plants are used to clean up pollutants, is also often an objective when transforming roots. These two examples are used to review potential effects of root genetic modifications on shoots. There are several examples in which root-specific genetic modifications only lead to better plant performance if the genes are specifically expressed in roots. Constitutive expression can even result in modified plants that perform worse than non-modified plants. Rhizosphere effects have rarely been examined, but clearly genetic modification of roots can influence rhizosphere interactions, which in turn can affect shoot properties. Indeed, field studies with root-transformed plants frequently show negative effects on shoots that are not seen in laboratory studies. This might be due to the simplified environments that are used in laboratories which lack the full range of plant–rhizosphere interactions that are present in the field.