This study was planned to identify differences in the milk metabolite composition of Indian (Sahiwal), exotic (Holstein-Friesian) and their crossbred cows in intensive system of management. To mimic the management system of ancient India, indigenous cattle under extensive system (zero input) were also included. Holstein-Friesian (HF) had significantly higher amount of saturated fatty acids (SFA, 76.3%) as compared to the crossbred (73.3%) and Sahiwal (68.0%). HF had the highest concentration (42.7%) of hypercholesterolemic fatty acids and the maximum value (68.5) of athrogenecity index (AI). Sahiwal had the highest proportion (32.1%) of total unsaturated fatty acids (UFA). Mineral, vitamin, n-3 fatty acids and total amount of essential amino acids did not vary across the three groups. Milk of indigenous cattle maintained only on grazing had more favorable nutrient profile. It had low SFA (61.4%), high UFA (38.6%) and higher concentrations of both monounsaturated fatty acids (31.4%) and polyunsaturated fatty acids (7.2%). The n-6/n-3 ratio (2.7) and the AI (33.9) were significantly lower. Significantly higher concentrations of minerals (Zn, Fe, P and Cu) and vitamins except vitamin B5 were recorded in their milk. The study revealed that milk metabolite characteristics can be used to promote indigenous cattle.