Fumonisins are strongly toxic metabolites of Fusarium proliferatum and Fusarium verticillioides commonly present in corn-based feed. The aim of the study was to evaluate bone homeostasis in experimental fumonisins B1 and B2 intoxication of rats, a vertebrate animal model of toxicological studies, as still little is known about the possible disturbing effect of fumonisins on bone homeostasis. Adolescent (5-week-old) male Wistar rats were randomly assigned into a control group and a group FB intoxicated with fumonisins by daily intragastric administration of fumonisins at the dose of 90 mg/kg of body weight per animal in the FB group for 21 days. The fumonisin intoxication did not affect body and bone mass, although the mechanical and geometric properties were decreased in fumonisin-intoxicated rats. Bone volumetric and mineral density did not differ between groups, but bone mineral content and bone ash percentage was lower in the FB group. Detailed analysis showed that Ca, Cu, Fe, Mn, Sr, and Zn bone content significantly decreased in fumonisin intoxicated rats and the alterations in structure of bone mineral phase (reduction of the apatite-bone crystals size) were noted. While the negative structural alterations in growth plate and articular cartilages were also observed, fumonisin intoxication improved histomorphometrical parameters of trabecular bone. Concluding, the dose of fumonisins used in the present study caused hepatotoxic effect, which was sufficient to trigger the disturbance in mineral homeostasis resulting in altered bone metabolism and decreased mechanical endurance.