Nanomaterials composed of silver (Ag), copper-doped titanium dioxide (Cu-$TiO_2$), and pure titanium dioxide ($TiO_2$) have wide applications in consumer products such as cosmetics, electronic appliances, clothes, and industry materials such as solar cell. However, there are problems associated with the exposure of aquatic organisms in the ecosystem to such nanomaterials. In this study, we investigated the expression pattern of genes in zebrafish embryos after exposure to nanomaterials. We used several functional categories including apoptosis, endocytosis, immune response, and endoplasmic reticulum stress so on. A total of 314 (278 up-regulated and 36 down-regulated), 283 (129 up-regulated and 154 down-regulated), and 360 (198 up-regulated and 162 down-regulated) genes were differentially expressed in zebrafish embryos exposed to Ag, Cu-$TiO_2$, and $TiO_2$ NPs, respectively, with apoptosis being the function of the highest proportion of differentially expressed genes in all 3 NP exposures. Our data provide a basis for conducting further mechanistic studies of genes that are induced or suppressed upon exposure to NPs in zebrafish embryogenesis.