Whole-body vibrations (WBV) are a potentially harmful non-chemical pollutant that can have severe effects on developing embryos, especially during the first semester of pregnancy, when organisms are most susceptible to defects and abnormalities. In this study, we established the zebrafish as a laboratory-based animal model to provide an in-depth evaluation of the effect of exposure to WBV on the bone tissue of a living organism, during bone development. Zebrafish embryos and larvae were exposed to low-frequency WBV, ranging between 10 and 20Hz, for up to 4 days. Despite their mildness, these treatments were sufficient to induce a wide array of skeletal defects in zebrafish larvae. Depending on the developmental stage at which the exposure to WBV was started (from 10 hours post-fertilization to 5 days post-fertilization), the skeletal elements of zebrafish larvae were affected differently. The observed phenotypes ranged from missing bone elements to bone fusions, and varied depending on the type of bone that was affected. These results indicate that exposure to WBV during embryonic development can affect the normal skeletal development in vertebrates.