We prepared oligodeoxynucleotides (ODNs) possessing a 5-fluorodeoxyuridine (5-FU) unit as a 19F-signal transmitter, and characterized their structures including single strand, duplex, and triplex using 19F NMR. The change in chemical shift induced by incorporation of 5-FU into the ODNs and the formation of higher order structures allowed monitoring of structural changes. Data from UV melting experiments and CD spectra were consistent with the spectral changes in the NMR studies. These 19F-labeled ODNs may be promising molecular probes for the identification of DNA structures in complicated biological conditions.