The vertebrate body displays a segmental organization which is most conspicuous in the periodic organization of the vertebral column and peripheral nerves. This metameric organization is first implemented when somites, which contain the precursors of skeletal muscles and vertebrae, are rhythmically generated from the presomitic mesoderm (PSM). Somites then become subdivided into anterior and posterior compartments essential for vertebral formation and segmental patterning of the peripheral nervous system1–4. How this key somitic subdivision is established remains poorly understood. Here we introduce novel tridimensional culture systems of human pluripotent stem cells (PSCs), called Somitoids and Segmentoids, which recapitulate the formation of somite-like structures with antero-posterior (AP) identity. We identify a key function of the segmentation clock in converting temporal rhythmicity into the spatial regularity of anterior and posterior somitic compartments. We show that an initial salt-and-pepper expression of the segmentation gene MESP2 in the newly formed segment is transformed into compartments of anterior and posterior identity via an active cell sorting mechanism. Our work demonstrates that the major patterning modules involved in somitogenesis including the clock and wavefront, AP polarity patterning and somite epithelialization can be dissociated and operate independently in our in vitro systems. Together we define a novel framework for the symmetry breaking process initiating somite polarity patterning. Our work provides a valuable platform to decode general principles of somitogenesis and advance knowledge of human development.