We describe an integrated system setup for HIFU and MRI thermometry for mouse experiments. The applications of such a system include MRI imaging and thermometry for evaluation and feedback during HIFU applications on mouse models of various diseases; and validation of temperature estimated by other methods, such as RF data. A 5 MHz geometrically focused (diameter of 16.1mm, focal length 35mm), MRI-compatible HIFU transducer is used, driven by a programmable signal generator and a power amplifier. The small animal MRI scanner has been programmed to acquire sequential phase information, which is used to determine frequency shift. Relative temperature rise is then calculated by proton resonance frequency (RPF) method. The current software development is done in C++ and Matlab. An integrated software is being developed to streamline the acquisition, analysis and visualization during HIFU delivery. Preliminary experiments have been performed using different phantoms. Performing HIFU (less than 100 watts) under MRI has had minimal interference for MRI data acquisition. The development is continuing for further characterizing and understanding the interference at the higher power level and accelerate data acquisition rate to achieve thermometry for a few frames per second. Further tissue experiments are under way with target of live mouse experiments. We present the overall design and discuss challenges encountered in the development of such system for experiments on mouse.