Pharmacokinetic study of small interfering RNA (siRNA) is an important issue for the development of siRNAs for use as a medicine. For this purpose, a novel and favorable positron emitter-labeled siRNA was prepared by amino group-modification using N-succinimidyl 4-[fluorine-18] fluorobenzoate ([(18)F]SFB), and real-time analysis of siRNA trafficking was performed by using positron emission tomography (PET). Naked [(18)F]-labeled siRNA or cationic liposome/[(18)F]-labeled siRNA complexes were administered to mice, and differential biodistribution of the label was imaged by PET. The former was cleared quite rapidly from the bloodstream and excreted from the kidneys; but in contrast, the latter tended to accumulate in the lungs. We also confirmed the biodistribution of fluorescence-labeled naked siRNA and cationic liposome/siRNA complexes by use of a near-infrared fluorescence imaging system. As a result, a similar biodistribution was observed, although quantitative data were obtained only by planar positron imaging system (PPIS) analysis but not by fluorescence in vivo imaging. Our results indicate that PET imaging of siRNA provides important information for the development of siRNA medicines.