SummaryThe root is an excellent model for studying developmental processes that underlie plant anatomy and architecture. Its modular structure, the lack of cell movement and relative accessibility to microscopic visualization facilitate research in a number of areas of plant biology. In this review, we describe several examples that demonstrate how cell type‐specific developmental mechanisms determine cell fate and the formation of defined tissues with unique characteristics. In the last 10 yr, advances in genome‐wide technologies have led to the sequencing of thousands of plant genomes, transcriptomes and proteomes. In parallel with the development of these high‐throughput technologies, biologists have had to establish computational, statistical and bioinformatic tools that can deal with the wealth of data generated by them. These resources provide a foundation for posing more complex questions about molecular interactions, and have led to the discovery of new mechanisms that control phenotypic differences. Here we review several recent studies that shed new light on developmental processes, which are involved in establishing root anatomy and architecture. We highlight the power of combining large‐scale experiments with classical techniques to uncover new pathways in root development. Contents Summary 26 I. Introduction 26 II. Signaling modules that regulate cell fate 27 III. Understanding global connections through gene regulatory networks 29 IV. Signaling mechanism of organ formation: lateral root formation 32 V. Genetic regulation of global root architecture 33 VI. Conclusions 35 References 36