Apparatus for aligning an ablation catheter and a temperature probe relatively for an ablation procedure includes an ablation catheter with a first antenna for ablating tissue at an ablation site in a patient's body and a temperature probe for placement in a body passage having a wall portion adjacent to the ablation site so that a second antenna in the probe is positioned opposite the first antenna. A microwave source provides a pulse modulated microwave signal to one of the antennas and a radiometer is in circuit with the other antenna. A synchronizing device in circuit with the microwave source and the radiometer enables the radiometer to synchronously detect the microwave signal so that the radiometer provides an alignment signal whose strength reflects the degree of alignment of the first and second antennas which signal may be used to control an alignment display. An alignment method using the apparatus is also disclosed.