The use of genetically modified (GM) plants in agriculture has been a topic in public debate for over a decade. Despite their potential to increase yields, there may be unintended negative side-effects of GM plants on soil micro-organisms that are essential for functioning of agro-ecosystems. Fungi are important soil organisms and can have beneficial or harmful effects on plants. Their benefits to agro-ecosystems come from their activities as free-living saprobes breaking down soil organic matter thereby releasing nutrients to the crops, as well as from mutualistic interactions. On the other hand, soil-borne plant pathogenic fungi can cause severe damage in crops. Understanding of the impact of GM plants on the dynamics and functioning of soil fungi is essential to evaluate the possible risks of introduction of GM plants for ecosystem functioning. In recent years, over 50 studies have addressed the effects of various GM traits in crops on soil fungal community structure and function. These studies showed that GM crops can have positive, negative, or neutral effects on both free-living and plant-associated soil fungi. The observed discrepancy in results of these studies is discussed. This is done by highlighting a number of case studies. New methods developed in recent years have enabled microbial ecologists to get a better picture on the functioning and assembly of soil fungal communities. This review presents and discusses two of the most promising methods which are also readily usable in risk assessment of GM plants on soil fungi and that could help answer remaining key questions in the field.