Rotavirus (RV) is considered to be one of the major causes of acute episodic diarrhoea throughout the world. This study was undertaken to investigate the effect of soybean trypsin inhibitor (TI) on brush-border enzymes during rotavirus infection in protein energy malnourished (PEM) infant mice. Animals were divided into 4 groups, namely controls, PEM, PEM+RV and PEM+RV+TI (n = 36 each). Group 1 and 2 animals were orally inoculated with 50 µl of normal saline each. Group 3 animals were orally inoculated with 50 µl of 100 ID50 dose of RV stock each. Group 4 animals were similarly inoculated with 0.6 mg TI/g body weight along with 50 µl of RV stock each. Animals were examined daily for diarrhoea and their body weight was recorded on alternate days postinoculation (dpi). Animals were killed by cervical dislocation after being given light chloroform anesthesia on 0, 1, 3, 5, 7 and 10 dpi. Small intestines were excised and homogenized in normal saline. Proteins, gammaglutamyl transpeptidase, alkaline phosphatase and disaccharidases were estimated in jejunum and ileum. Body weight was significantly reduced in PEM animals and with RV infection. Histologically, focal areas of vacuolar degeneration of lining epithelium were seen in RV-infected animals. Disaccharidases and other enzyme activities were decreased significantly in the PEM group compared to healthy controls and further depressed with RV infection in malnourished animals as compared to non-infected PEM. The enzyme activities were restored in animals receiving TI along with RV compared to the group receiving RV without TI. With the administration of soybean TI, the activities of disaccharidases, alkaline phosphatase, gammaglutamyl transpeptidase and intestinal architecture were restored showing a protective effect in PEM during RV infection.