Modification of proteins by enzymes such as Transglutaminase (TG) has recently become of great interest to food scientists. TG induced cross-linking has strong effects on the functionality of milk proteins. Effect of TG on heat stability, antioxidant activity, surface hydrophobicity, rennet coagulation time, emulsifying and foaming properties of cow and buffalo milk proteins was studied. TG treatment improves heat stability from 18 min to 38 min in cow milk and 14.5 min to 25.5 min in buffalo milk, surface hydrophobicity from 237.28 to 292.23 in cow milk and 252.8 to 332.7 in buffalo milk. Cross-linked cow and buffalo casein shows better emulsifying and foaming properties. It does not affect the antioxidant activity of milk proteins. Whereas cross-linked milk proteins are highly resistant to rennet coagulation. TG treatment completely prevents rennet coagulation of cow milk, whereas in buffalo milk rennet coagulation time gets elongated.