In numerous studies dealing with roots of woody plants, a description of the root system architecture is needed. During the twentieth century, several manual measurement methods were used, depending on the objectives of study. Due to the difficulties in accessing the roots and the duration of measurements, the studies generally involved a low number of root systems, were often qualitative and focused only on one specific application. Quantitative methods in plant architecture were largely developed in the last 40 years for aerial architecture. However, root systems have particular features and often need specific procedures. Since the end of the 1990s, new devices and techniques have been available for coarse root architecture measurements including volume location techniques (non-invasive or destructive) and manual or semi-automatic 3D digitising. Full 3D root system architecture dynamics was also reconstructed from partial measurements using modelling procedures. On the one hand, non-invasive and automatic techniques need more development to obtain full 3D architecture, i.e. geometry and topology. On the other hand, both one inexpensive manual and one semi-automatic digitizing procedure are now available to measure precisely and rapidly the full 3D architecture of uprooted and excavated coarse root systems. Specific software and a large number of functions are also available for an in-depth analysis of root architecture and have already been used in a dozen of research papers including a fairly large sample of mature trees. A comprehensive analysis of root architecture can be achieved by classifying individual roots in several root types through architectural analysis. The objective of this paper is both to give a detailed overview of the state of the art techniques for 3D root system architecture measurement and analysis and to give examples of applications in this field. Practical details are also given so that this paper can be used as a sort of manual for people who want to improve their practice or to enter this quite new research field.