Recent studies using Arabidopsis propose a framework of root development and pattern formation that can be divided to three processes. First, a positional signal that is delivered from neighboring cells controls the fate of undifferentiated cells. Then, cell fate is fixed through a protein-network that includes various transcription factors. Finally, the expression of a particular gene-set leads to fate-dependent cell differentiation, resulting in oriented cell division, cell specification and cell elongation. In addition, these processes could be modified by chromatin stabilization and protein degradation. We focus on three fundamental patterns of root development, circumferential pattern, radial pattern and proximo-distal pattern, and on novel approaches to identify genes that are responsible for the spatiotemporal regulation of root development.