Recent findings in a clinical trial in which an adeno-associated virus (AAV) vector expressing coagulation factor IX (F.IX) was introduced into the liver of hemophilia B subjects highlighted a new issue previously not identified in animal studies. Upon AAV gene transfer to liver, two subjects enrolled in this trial developed transient elevation of liver enzymes, likely as a consequence of immune rejection of transduced hepatocytes mediated by AAV capsid-specific CD8(+) T cells. Studies in healthy donors showed that humans carry a population of antigen-specific memory CD8(+) T cells probably arising from wild-type AAV infections. The hypothesis formulated here is that these cells expanded upon re-exposure to capsid, i.e. upon AAV-2 hepatic gene transfer, and cleared AAV epitope-bearing transduced hepatocytes. Other hypotheses have been formulated which include specific receptor-binding properties of AAV-2 capsid, presence of capsid-expressing DNA in AAV vector preparations, and expression of alternative reading frames from the transgene. Absence of a valid animal model has prevented an in-depth mechanistic study of the phenomenon. Several possible solutions to the problem are discussed, including the administration of a short-term anti-T cell immunosuppression regimen concomitant with gene transfer. While more studies will be necessary to further define mechanisms and risks associated with capsid-specific immune responses in humans, monitoring of these responses in clinical trials will be essential to achieving the goal of long-term therapeutic gene transfer in humans.