The present study established the feasibility of a technique for monitoring focused ultrasound (FUS) lesion formation in vivo using localized harmonic motion (LHM) measurements. Oscillatory motion (frequencies between 50 and 300 Hz) was generated within tissues by induction of a periodic radiation force with a FUS transducer. The harmonic motion was estimated using cross correlation of RF ultrasonic signals acquired at different instances during the motion by using a confocal diagnostic ultrasound transducer. The technique was evaluated in vivo in rabbit muscle (14 locations) in an magnetic resonance (MR) imager for simultaneous ultrasound harmonic motion tracking and MR thermometry. The measured maximum amplitude of the induced harmonic motion before and after the lesion formation was significantly different for all the tested motion frequencies, and decreased between 17 and 81% depending on the frequency and location. During the FUS exposure a drop in the maximum amplitude value was observed and a threshold value could be associated to the formation of a thermal lesion. A series of controlled sonications was performed by stopping the exposure when the threshold value in LHM amplitude was reached and the presence of a thermal lesion was confirmed by MR imaging. LHM measurements were also used to perform a spatial scan of the tissues across the exposure region and the thermal lesions could be detected as a reduction in the maximum motion amplitude value at the sonication region.