In this study, we investigated the effects of $TiO_2$ nanoparticles, potential biological toxins, on zebrafish (Danio rerio) embryogenesis. We exposed zebrafish embryos to $TiO_2$ particles of three different diameters (12-14 nm, 80-100 nm, 150-200 nm) and compared the acute responses of the embryos during embryogenesis. Scanning electron microscope (SEM) images demonstrated that 12-14 nm $TiO_2$ particles were small ball types, while 80-100 nm $TiO_2$ particles were square and ball types. Square layers were observed in the 150-200 nm $TiO_2$ particles. The zebrafish morphants survived that exposure to the $TiO_2$ nanoparticles exhibited incomplete notochord formation, with epidermal injuries observed in larvae exposed to 12-14 nm and 150-200 nm particles. In microarray analysis, several genes involved in immune response, tumor necrosis factor, and endocytosis and its regulation were differentially expressed in accordance to the nanoparticle size. Gene expression in embryos exposed to 12-14 nm particles was significantly upregulated in comparison to the control group and embryos exposed to other particle sizes. The results of the present study suggest that Ti02 nanoparticles 12-14 nm in size have toxic effects on zebraish development. $TiO_2$ nanoparticles of larger sizes (80-100 nm, 150-200 nm) exhibit different types of genetic effects.