This protocol details our approach to removing the native thymus from an NSG mouse. The NSG mouse thymus is atrophied, but through experiments in our lab, we have found that these thymi are still functional and capable of producing CD3+ cells. Removal of these native thymi prevents the production of CD3+ cells in NSG mice if a replacement thymus is not implanted. Due to their atrophic state, the native thymi are difficult to visualize during surgery and much practice is required to reduce mortality during the operation.