Giant South American turtles (Podocnemis expansa) are at a risk of extinction because of the rapid decline in their population over the last few decades. Metabolic bone disease (MBD) is common in captive testudines, but is often not diagnosed until a later stage. The authors present the cases of four captive giant South American turtles with carapace deformity secondary to MBD that underwent computed tomography (CT) scans of the carapace bones and vertebral column. Findings indicative of changes in geometry were found in both. The cancellous bone pattern was characterized by varying degrees of increased trabecular spacing and cortical thinning of the pleural bones. Bone densitometry analysis of the pleural and neural bones and at the level of the body of the third, fourth, and fifth dorsal vertebrae showed mean density values much lower than those found in two adult specimens of the same species that were considered healthy. In conclusion, CT contributed important information on the degree of demineralization and possible structural changes due to MBD and should be considered a relevant tool for diagnosis of this condition.