To study the effect of Whey Preparation on intestinal mucositis, model developed by administration of single dose of etoposide (60mg/Kg body wt., i.p). The experimental procedure included Adult albino rats (10±1 week old) of Wistar strain (n=30, 6/group). Freshly prepared whey preparation-(100 and 200mg/Kg/body wt.) was administered by orogastric gavage- Pre, both pre and post etoposide injection. Effectiveness of whey preparation was determined by estimating the biochemical parameters including intestinal Tumor Necrosis Factor-α, Interleukin-6, sodium potassium ATPase, inflammatory markers- Cyclooxygenase and Myeloperoxidase along with Nitric Oxide and reduced Glutathione with and without intervention after 72 hrs. of etoposide injection. There was a significant increase in the Tumor Necrosis Factor –α, Interleukin-6 levels and extent of apoptosis in etoposide controls. Etoposide administration caused a significant decreased the activity of Na+-K+ ATPase and reduced glutathione levels in intestinal tissue. However, in the post treatment groups, Tumor Necrosis Factor–α, Interleukin-6 as well as extent of apoptosis were reverted to normal after whey preparation administration.Whey Preparation gavage in both the study groups- pre and both pre and post etoposide exposure showed that intervention was able to preserve/ prevent changes in the biochemical activity. The results support the WP potentials to reduce the deleterious effects of etoposide on normal cells, which leads to mucositis.