The primary axis and main tissue types of Arabidopsis are laid down in the early embryo. Apical-to-basal auxin flux functions as a global organizer of the axis, and recent reports are clarifying our mechanistic understanding of how a graded auxin distribution is generated and interpreted. Polar targeting of PIN transporters in the cells of the embryo is dynamic and linked to their phosphorylation status, suggesting a flexible mechanism for regulating auxin flux in space and time. PLETHORA transcription factors then interpret the graded auxin distribution to provide positional values along the axis in a dose-dependent manner. A comparable framework for tissue patterning in the radial dimension is still lacking, although cell surface signaling probably plays a key role.