Cell replacement has the potential to become a frontline therapy to remedy behavioral impairments in Huntington’s disease. To determine the efficacy of stem cell transplantation, behavioral assessment and in vivo monitoring of the lesion environment are paramount. We here demonstrate that neural stem cells from the MHP36 cell line prevented the development of a deficit on the beam walk test while providing partial recovery of learning in the water maze. However, no beneficial effect on rats’ impairment in the staircase test was observed. By quantification of the lesion from serial magnetic resonance images, no effect of neural stem cells on lesion volume was observed. Instead, a preservation of striatal volume over time and its correlation with performance on the beam walk test suggested that sparing of behavioral function was associated with a stagnation of ongoing tissue loss rather than a reduction in lesion size. Serial imaging therefore warrants further implementation in clinical trials of neural grafts to monitor in vivo changes in the damaged brain due to transplantation.