Fumonisins (FB) are metabolites found in cereal grains (including maize), crop products, and pelleted feed. There is a dearth of information concerning the effects of FB intoxication on the intestinal histomorphometry, the expression of intestinal tight junction proteins, and the bone structure and liver in pre-laying hens. The current experiment was carried out on hens from the 11th to the 14th week of age. The hens were orally administered an extract containing fumonisin B1 (FB1) and fumonisin B2 (FB2) at doses of 0.0 mg/kg b.w. (body weight), 1.0 mg/kg b.w., 4.0 mg/kg b.w., and 10.9 mg/kg b.w. for 21 days. Following FB intoxication, the epithelial integrity of the duodenum and jejunum was disrupted, and dose-dependent degenerative changes were observed in liver. An increased content of immature collagen was observed in the bone tissue of FB-intoxicated birds, indicating intensified bone turnover. A similar effect was observed with regards to the articular cartilage, where enhanced fibrillogenesis was observed mainly in the group of birds that received the FB extract at a dose of 10.9 mg/kg b.w. In conclusion, FB intoxication resulted in negative structural changes in the bone tissue of the hens, which could result in worsened bone mechanics and an increase in the risk of bone fractures. Fumonisin administration, even at a dose of 1.0 mg/kg b.w., can lead to degradation of the intestinal barrier and predispose hens to intestinal disturbances later in life.