Allografts continue to be used in clinical neurotransplantation studies, hence it is crucial to understand the mechanisms that govern allograft tolerance. We investigated the impact of transplantation site within the brain on graft survival. Mouse (FVB) glial precursors, transfected with luciferase have been injected (3×105) into the forceps minor (FM) or striatum (STR). Immunodeficient rag2−/− and immunocompetent BALB/c mice were used as recipients. Magnetic resonance imaging confirmed that cells were precisely deposited at the selected coordinates. The graft viability was assessed non-invasively with bioluminescent imaging for a period of 16 days. Regardless of implantation site all grafts (n=10) deposited in immunodeficient animals revealed excellent survival. In contrast, immunocompetent animals accepted all grafts only at STR site (n=10), while all FM grafts were rejected (n=10). To investigate the factors that led to rejection of FM grafts, with acceptance of STR grafts, another group of animals (n=19) was sacrificed during pre-rejection period, on day 5. Near-infrared fluorescence imaging with IRDye®800CW-PEG probe displayed similar blood-brain barrier disruption at both graft locations. The morphological distribution of FM grafts was cylindrical, parallel to the needle track, while cells transplanted into the STR accumulated along the border between the striatum and corpus callosum. There was a significantly less infiltration by both innate and adaptive immune cells in the STR grafts, especially along the calloso-striatal border. With allograft survival being dependent on the transplantation site, the anatomical coordinates of the graft target should always be taken into account as it may determine success or failure of therapy.