A tunable microwave ablation catheter system is disclosed which matches the impedance of its power supply with the transmission line to minimize reflected power and optimize energy delivery to targeted tissues. The tuner itself may be located in the power supply, the transmission line or the antenna. Tuner mechanisms at these locations can change the antenna configuration, move material relative to the antenna or alter the waveguide. A controller monitors the catheter system operation. A method of medical treatment is disclosed where the impedances of the components of the systems are adjusted during use to compensate for impedance variations.