It is known that excess alcohol consumption during pregnancy can increase the risk of fetal alcohol spectrum disorder (FASD). However, the effect of ethanol exposure on bone morphogenesis in fetus is largely unknown. In this study, we demonstrated that ethanol treatment of gastrulating chick embryos could inhibit long bone (humerus, radius and ulna) development. Histological examination revealed that ethanol exposure reduced the width of the proliferation and hypertrophic zones. In addition, cell proliferation and alkaline phosphatase activities were repressed. We also investigated the effect on chondrogenesis and chondrogenesis was inhibited. Ethanol exposure also induced excess reactive oxygen species (ROS) production and altered the expression of osteogenesis-related genes. The inhibiting effect on flat bone (sclerotic ossicle) and the generation of cranial neural crest cells (progenitors of craniofacial bones) was also presented. In conclusion, ethanol exposure during the embryonic period retards bone development through excess ROS production and altered bone-associated gene expression.