Brazil is considered to be one of the largest consumers of pesticides in the world, and herbicides represent the most commonly used class of these products. Atrazine and glyphosate, the most important herbicides, contaminate the waters of several Brazilian rivers and are involved in organ and bone malformations in different species. Among the possible target organisms, reptiles may be indirectly affected by pesticide use once their natural habitats are rivers and streams. Therefore, the objective of this study was to assess the possible effects of exposure to the herbicides atrazine and glyphosate in bone ontogeny of Podocnemis expansa. Eggs were artificially incubated in sand moistened with water contaminated with atrazine at concentrations equal to 0, 2, 20, or 200 μg/L, and glyphosate at 65, 650 or 6,500 μg/L. In the control group, the substrate was moistened with distilled water. Two eggs were collected from each incubator every ten days until hatching. For the analysis of bone development, soft tissues were diaphanized, and bones and cartilages were stained with Alizarin red S and Alcian blue, respectively. Specimens were analyzed by stereomicroscopy. Morphological characteristics of the cartilages and bones of the embryos were compared with descriptions of normal ontogeny available in the literature for P. expansa embryos. No abnormalities were observed in bone ontogeny of any of the experimental groups.