Various microorganisms have been found to colonise the male genital tract which may play an important role in altering seminal parameters and thereby reducing male fertilizing potential. A total of 35 semen samples, obtained from PGIMER, Sector-12, Chandigarh, India were subjected to routine semen analysis according to WHO guidelines. The volume of all the samples, motility of 88.5% samples, pH of 80% of the samples was optimum. On culturing these samples on Brain Heart Infusion agar plates, it was found that 80% of the isolates so obtained were Gram positive cocci, 18% Gram negatives and 2% were yeast. Out of these isolates, 4% showed complete immobilization whereas 12% led to agglutination of spermatozoa. Scanning electron microscopy showed morphological alterations in sperm head, neck and mid piece etc. when incubated with the sperm immobilizing and sperm agglutinating strains. Further when the enzymatic activity was looked for, the results showed that these organisms were able to produce either protease, phospholipase, lipase or all of these. Hemolysis on sheep blood agar showed that only 2% of the isolates were capable of causing complete hemolysis and 6% showed partial hemolysis. The Gram positive bacteria were maximally sensitive to Oxacillin and Gram negative were sensitive to tobramycin and gentamycin. In conclusion, various Gram positive and Gram negative bacteria inhabiting male reproductive tract might produce certain factors which may impair sperm parameters. Eradication of these microbes by use of antibiotics can be a probable cure of microorganism induced infertility.