Arsenic usually accumulates in soil, water and airborne particles, from which it is taken up by various organisms. Exposure to arsenic through food and drinking water is a major public health problem affecting some countries. At present there are limited laboratory data on the effects of arsenic exposure on early embryonic development and the mechanisms behind its toxicity. In this study, we used zebrafish as a model system to investigate the effects of arsenite on early development. Zebrafish embryos were exposed to a range of sodium arsenite concentrations (0–10.0mM) between 4 and 120h post-fertilization (hpf). Survival and early development of the embryos were not obviously influenced by arsenite concentrations below 0.5mM. However, embryos exposed to higher concentrations (0.5–10.0mM) displayed reduced survival and abnormal development including delayed hatching, retarded growth and changed morphology. Alterations in neural development included weak tactile responses to light (2.0–5.0mM, 30hpf), malformation of the spinal cord and disordered motor axon projections (2.0mM, 48hpf). Abnormal cardiac function was observed as bradycardia (0.5–2.0mM, 60hpf) and altered ventricular shape (2.0mM, 48hpf). Furthermore, altered cell proliferation (2.0mM, 24hpf) and apoptosis status (2.0mM, 24 and 48hpf), as well as abnormal genomic DNA methylation patterning (2.0mM, 24 and 48hpf) were detected in the arsenite-treated embryos. All of these indicate a possible relationship between arsenic exposure and developmental failure in early embryogenesis. Our studies suggest that the negative effects of arsenic on vertebrate embryogenesis are substantial.