Cow urine is an excretory fluid of biological origin that reflects summary of events occurring in body as a result of changing physiology or pathological conditions. Historically bovine urine is in use for various applications. However, very limited work is available on scientific evaluation of its effectiveness. To explore the active principles behind the activity of cow urine we focused our investigation on endogenous peptides derived from cow urine from three important physiological states of Sahiwal cows viz. heifer, lactation and pregnancy. These peptides possess several bioactive properties such as antimicrobial, antiangiogenic, antioxidant antithrombotic etc. Endogenous peptides are small size peptides (<10 kDa) which were obtained by using ultra-filtration assembly with a 10 kDa molecular weight cut-off filter. The filtrate containing peptides were used in solid phase extraction (SPE) for separation of peptides. Our preliminary investigation showed that the extracted peptides are endowed with antimicrobial activity as confirmed by disk diffusion assay (6 mm discs coated with urinary peptides) on S. aureus. MS/MS analysis of the crude peptides extracted from SPE further revealed 6238, 5465 and 3773 peptides from heifer, lactation and pregnant respectively with 10 individual samples for each group. Amino acids composition profile of the peptide sequences from all the groups follows the same pattern with the alanine, glycine, leucine, proline and serine being the most abundant amino acids. Intrestingly, most of the sequences were derived from collagen protein. Nevertheless, the types of sequences are mostly unique to individual physiological states. Using several databases (CAMPR3, Antiinflam TumorHPD etc.) we predicted potential functions of peptides such as anti-hypertension, anticancer and antimicrobial activity. Our study suggests that the diverse roles of cow urine in various applications are possibly due to the wide diversity of peptides present in cow urine.