Top of pageAbstract First generation adenoviral vectors (RAd) transfer genes into the brain with high efficiency, and provide high levels and long term expression in the absence of priming of an anti-adenoviral immune response. Systemic immunization to the RAd induces a cellular adaptive immune response which eliminates the expression of the transgene from the brain, and causes a chronic inflammatory response. In order to elucidate the mechanisms by which the immune response clears transgene expression from the brain, we asked whether, following the delivery of RAds into the striatum, and systemic immune priming, the immune mediated inhibition of transgene expression: (i) reduces the levels of transgene transcripts, vector genome copy numbers, or both; (ii) was transgene dependent; (iii) was promoter dependent; and (iv) caused brain neurotoxicity. The answer to these questions can indicate the mechanisms by which the adaptive immune response controls transgene expression from viral vectors in the brain. Our experiments provided the following results: (1) Immune-mediated inhibition was transgene independent (both expression of b-gal or HSV1-TK were eliminated); (2) the immune system reduced the levels of mRNA encoding for the transgene by more than 90%, but genome copy numbers were only reduced by 10–20%; (3) activated lymphocytes entering the brain were equally efficient in inhibiting expression from viral murine-CMV, human-CMV, RSV promoters, the neuronal synapsin promoter, and the housekeeping b-actin promoter; (4) localized and statistically significant neurotoxicity was encountered in the substantia nigra, the area of the brain transduced following injection of viral vectors into the striatum. In summary, our data indicate that immune-mediated silencing of RAd-encoded transgene expression in the brain is transgene independent, promoter independent, and acts mainly by reducing the number of mRNA. Importantly, we were able to uncover a localized, but statistically significant reduction in the number of transduced neurons. This strongly suggests that activated lymphocytes exert transgene silencing in the brain through a combination of non-cytolytic, and to a lesser extent, also cytotoxic mechanisms.