RNA interference is an evolutionarily conserved gene silencing process triggered by double-stranded RNAs. Common to all cell types, is the production of 21-24 nucleotide small interfering RNA (siRNAs), which guide the RNA-induced silencing complex (RISC) to identify and cleave target mRNA sequences. Presently, this biological breakthrough method has revolutionised gene function studies and holds great promise as validating drug targets and treating human diseases. However, despite the success that has been achieved by this technology, studies carried in human blood cells have revealed that siRNAs could generate bystander effects, including the activation of innate immunity and inhibition of unintended target genes. Interestingly, 2' uridine-modified siRNAs did not trigger TLR signalling, but they totally suppressed immune activation by immunostimulatory siRNAs when both molecules where delivered to the same endosomes. This review describes the recent advances in understanding the innate immune response to both single and double-stranded siRNAs. Also, it highlights the spectrum of molecular strategies allowing the design of therapeutic siRNAs with minimal side effects.