A method for tracking locally the 3D motion of biological tissues is developed and applied to the correction of motion during high intensity focused ultrasound (HIFU) therapy. The motion estimation technique is based on an accurate ultrasonic speckle tracking method. A pulse-echo sequence is performed for a subset of the transducers of a phased array. For each of these sub-apertures, the displacement is estimated by computing the 1D cross-correlation of the backscattered signals acquired at two consecutive times. The local 3D motion vector is then computed using a inversion algorithm. This technique is experimentally validated in vivo on anesthetized pigs. The 3D motion of liver tissues is tracked in real-time. The technique is combined with HIFU sequences and a real-time feedback correction of the HIFU beam is achieved by adjusting the delays of each channel. The sonications "locked on target" are interleaved with very motion estimation sequences.