In the present study an attempt has been made to differentiate three cattle populations of North East states of India i.e. Tripura, Mizoram and Manipur based on morphometric traits, using canonical discriminant analysis to see whether they are similar or distinct. Data consisted of eight different morphometric traits of 383 indigenous cows from Tripura (136), Mizoram (71) and Manipur (176). Morphometric traits included body length, height at withers, heart girth, paunch girth, face length, ear length, horn length and tail length without switch. All the morphometric traits under study differ significantly in these populations except horn length. All the traits, values were lower in Tripura cows than that of Mizoram and Manipur cows. The stepwise discriminant analysis showed that height at withers, body length, ear length, tail length without switch, paunch girth and face length were the most discriminating traits in these three cattle populations. The pair wise Mahalanobis distances between Tripura and Mizoram, Tripura and Manipur and Mizoram and Manipur were 9.72578, 5.72089 and 4.65239, respectively, and significant. The dendogram showed that there are two clusters; cluster one includes Manipur and Mizoram cows and cluster two Tripura cows those are clearly separated from cluster one. The Individual assignment of different cattle populations by the cross-validation classification revealed 84.13% of Tripura cows, 82.09% of Mizoram cows and 79.87% Manipur cows were assigned correctly into their respective population. Based on the present study we cannot conclude that they are three different distinct breeds. However, the present information on the three cattle populations could therefore be exploited in designing appropriate strategies for their management and conservation.