Expression of 11 genes of the Hox cluster (SiHox1, 2, 3, 5, 6, 7, 8, 9/10, 11/13a, 11/13b, and 11/13c) was assessed in the sea urchin Strongylocentrotus intermedius at early developmental stages, including the blastula (13 h post fertilization (hpf)), gastrula (35 hpf), prism (46 hpf), and pluteus (4 and 9 days post fertilization (dpf)) stages. Expression of SiHox7, 11/13b, and 11/13c was observed at the blastula stage; early activation of 11/13c was detected for the first time in regular sea urchins. The expression level was very low at the gastrula and prism stages. The pluteus stage showed a significant increase in expression of all Hox cluster genes. Deviations from temporal collinearity of Hox gene expression in echinoderms are discussed.