This review is devoted to analyzing design rules, as well as quality controls, in the development of highly effective and specific short interfering RNA (siRNA). Four crucial steps in the development of this siRNA are discussed, i.e., selecting target RNA and designing sense and antisense strands, as well as assessing the activity and specificity of corresponding siRNA. Special consideration is given to the principles of siRNA construction based on both structural and thermodynamical features and the nucleotide composition of siRNA, as well as structural and thermodynamical properties of target RNA and features of experimental performance. Bioinformatics resources for developing siRNA are also discussed. Information from this review can be useful for the development of highly effective and specific siRNA, short hairpin RNA (shRNA), and/or artificial microRNA (amiRNA) sequences for experimental gene therapy and functional genomics.