For two decades, genetic engineering has made it possible to develop crops and trees designed for yield improvement and simplified culture management. This, combined with field deployment of monocultures over large areas, can result in environmental stress and unwanted potential side effects. The commercial production of genetically modified (GM) crops and the recent development of GM trees raise concerns about their potential impact on the environment, in general, and on the biodiversity of non-target organisms, in particular. Fungi are spread worldwide and play key roles in ecosystems. They have been closely associated with plants since they emerged from the oceans. This review critically examines research monitoring the potential effects of GM crops and GM trees on target and non-target fungi. Parsing public databases for peer-reviewed publications about GM plant impacts on fungi yielded 149 studies, a relatively modest number considering the diversity of crops and ecosystems studied. Analysis of these publications showed that the effects of GM plants expressing herbicide and insect tolerance on fungi are understudied while they dominate the GM area worldwide. Experiments monitoring the impact of GM crops and GM trees with enhanced antifungal activity towards target fungi showed, for the most part, significant decreases in disease severity caused by fungal pathogens. Significant changes, expressed as an increase or decrease in fungal development, abundance, and diversity of non-target fungi, were observed in 18 out of 60 studies and all of them involved GM plants expressing traits that were unexpected to affect fungi. The remaining 42 studies did not identify a significant impact on fungal populations. Therefore, in spite of the fact that GM plants have been commercialized since 1996, no clear generalized trend can be identified and it appears that a case-by-case approach is the safest.