Plant root systems play a crucial role in ecosystems, radically impacting everything from nutrient cycling to species composition. Despite their importance, scientists are just beginning to develop the tools to understand how these complex systems are structured, how they function, and how structure and function are related. Much of the research into root systems today uses sophisticated new technologies to address basic questions and descriptions. A recent special issue of Applications in Plant Sciences contains six papers from the cutting edge of root science, exploring questions from the subcellular to the ecosystem level.