Balucatherium still bears the hallmarks of its Hyracodont ancestry. The molar teeth of the Balucatherium show the same pattern of the more primitive Hyracodont, only the teeth are much larger. This similarity occurs for the incisors also. Although much larger, the incisors of the Balucatherium are conical as are those of the Hyracodonts.

One surprising fact about Balucatherium is that it retained long and stretched toe bones as if it were a runner. This is surprising because other large animals, such as elephants and dinosaurs, show a shortening of the foot bones. The foot bones usually become stubby, square blocks, or flattened like pancakes. Animals this large had no need to run from any predator. Besides, Balucatherium was too large to run efficiently anyway. Thus, Balucatherium remains a good example of how animals sometimes retain ancestral features long after the body part has become useless.

The bone structure of Balucatherium was similar to some of the large dinosaurs. The vertebrae of the back and of the long neck were sculpted into hollows and struts. A structure such as this would have kept the weight down while retaining the strength. The weight of Balucatherium was supported over three toes which is the normal pattern for most rhinoceroses. What was missing from Balucatherium was the horn that most rhinoceroses have. In fact, the nasal bones of Balucatherium were quite weak.