Sterilization capability of 2.45GHz Electron Cyclotron Resonance plasma system on silicone catheter is investigated for Ar and N2 gas discharges. E.coli, MRSA, Basillus cereus and Bacillus subtilis bacteria infected silicone catheter pieces are tested for sterilization. Basillus subtilis, which is a spore type bacteria, is determined as the most resistant one, and non spore type bacteria, Escherichia coli, is determined as the easiest one. The results show that nitrogen -N2 discharge has better sterilizing effects than Ar discharge by 15% less in time. Doubling the applied microwave source power decreases sterilization time scanty. Sterilization of silicone catheter is less than an hour for above bacteria types. Plasma discharge sterilization preserves the chemical integrity of polymer - based instruments.