Risk assessment concerns and recent advances in microbial ecology have spurred a wave of research on the impact of genetically modified (GM) crops on soil-borne microbial community structure and function. Effects have often been observed, but these usually pale in comparison with 'normal' sources of variation. In spite of our incomplete knowledge of the microbial communities and processes in plant?soil systems, recent technological and conceptual improvements do offer a way forward. We propose a case-by-case approach within a framework that targets both potentially vulnerable indicators as well as general community parameters for assessing the impact of GM plants on soil microorganisms.