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Visceral organs of vertebrates positioned in a specific left-right asymmetric way. The most supported theory about mechanisms of body plan symmetry breakage links establishment of left-right asymmetry with directed extracellular fluid flow, generated by mono-ciliated cells in the so-called left-right organizer (LRO). LRO structures were found in various taxa across of vertebrates, which assume cilia-based mechanism of body symmetry breakage is conservative. One major question remained unanswered: where and when in evolution this mechanism was evolved. For our studies, we chose echinoderms, the basal Deuterostome animals and sister group to Chordata. It was shown that cilia in sea urchin archenteron (LRO homolog) during gastrulation play a crucial role in the spatial positioning of Nodal signaling. We use descriptive approaches to characterize differences in the LRO organization during development of three echinoderms: Paracentrotus lividus, Strongylocentrotus pallidus and Asterias rubens. The most striking differences we found between sea urchins and sea stars. We revealed that they have significantly different dynamics of the cilia formation in the archenteron. At the beginning of gastrulation of the A.rubens, the vegetal plate does not lose cilia as it happens in sea urchins but starts to invaginate with outer surface cilia. Surprisingly, the length of these cilia exceeds the diameter of archenteron. And apparently, such lengths of the cilia are not able to generate directional fluid flow. Our ultrastructural data let us suggest the absence of dynein arms in the structure of these cilia, and accordingly their motility. The expression patterns of motile cilia markers have been analyzed.