Recombinant adeno-associated virus (rAAV) is one of the most commonly used vectors for gene therapy. Despite the promising safety profile demonstrated in preclinical trials, the clinic efficacy of using rAAV was hampered by undesired response from the immune system. It is important to understand the mechanisms that lead to the induction of immune response against rAAV. Although a crucial role for innate immunity is shaping adaptive immune responses, the innate immune to rAAV was ignored in the past. Till now, at least three human cell types (dendritic cells, macrophages and endothelial cells) were discovered to be involved in sensing rAAV infection. The engagement of TLR9 by rAAV vector genomes triggers the activation of NF-kappaB signaling cascades, leading to the induction of pro-inflammatory cytokine genes. The viral capsid components are detected by TLR2, and this leads to the production of type I interferon mediated by interferon regulatory factors (IRFs) pathway. Self-complementary rAAV vectors induced higher TLR9 dependent innate immune response than single stranded rAAV. This review highlights the recent findings regarding the innate immune responses to rAAV vectors, the signaling pathways involved, and the impacts of innate immunity on the adaptive immune response to rAAV and its transgene expression.