Small interfering RNAs (siRNAs) have become the experimental tool of choice to suppress gene expression in a wide variety of organisms. Site selection and optimization does not appear to be as difficult for siRNAs as would be expected from historical experience with antisense oligonucleotides. Nevertheless, not all sites within a target gene perform equally. Significant progress has been made in defining sequence features that contribute to siRNA potency, and a variety of computational tools are available from academic and commercial sources to assist with siRNA design. Potential siRNA sequences should be screened for homology to other genes within the target organism's transcriptome to minimize cross-hybridization and inadvertent knockdown of unrelated genes via off-target effects. In addition to rational design criteria, chemical modification of the RNA can improve function by improving stability, reducing the potential for off-target effects and avoiding stimulation of the innate immune system.