To investigate of histopathologic and biochemical effects of caffeine citrate in newborn rats with hypoxia/reoxygenation (H/R)-induced intestinal injury. Materials and methods: One-day-old, 32 Wistar albino newborn rats (n=8) were randomly divided into four groups: control group (group1, n=8), caffeine group (group2, caffeine citrate administered subcutaneously, n=8), H/R group (group3, exposed to H/R, n=8), and caffeine + H/R group (group4, caffeine citrate administered and exposed to H/R, n=8). Caffeine citrate was initiated at a loading dose of 20 mg/kg, followed by a maintenance dose of 5 mg/kg/day, subcutaneously. On day 4 th , all animals except for groups 1 and 2 were exposed to H/R and sacrificed 6 hours after H/R procedure. Histopathological injury scores (HISs), interleukin-6 (IL-6), tumor necrosis factor-alpha (TNF-α), and oxidative stress index (OSI: total oxidant status "TOS"/total antioxidant status "TAS") levels were measured in intestinal samples. Results: As histopathological, the most severe damage was observed in H/R-induced groups (p<0.01). Although not statistically significant, the mean HISs of caffeine group was higher than the control group and lower than the H/R group. The levels of TNF-α, IL-6 and OSI in the groups 2, 3 and 4 were significantly higher than the control group (p<0.05). However, these biochemical parameters in the caffeine group were significantly lower than those of the H/R-induced groups (p<0.01). Conclusion: This study showed that caffeine citrate significantly increased the intestinal tissue levels of TNF-α, IL-6, and OSI. As a result, caffeine may be a predisposing risk factor for developing intestinal injury.