Progress in the development of advanced materials strongly depends on continued efforts to miniaturizing their structures; thus, a great variety of nanostructured materials are being developed nowadays. Metallic nanowires are among the most attractive nanometer-sized materials because of their unique properties that may lead to applications as interconnectors in nanoelectronic, magnetic, chemical or biological sensors, and biotechnological labels among others. A simple method to develop self-ordered arrays of metallic nanowires is based on the use of nanoporous anodic alumina (NAA) and self-assembled nanotubular titanium dioxide membranes as templates. The chemical characterization of nanostructured materials is a key aspect for the synthesis optimization and the quality control of the manufacturing process. In this work, the analytical potential of pulsed radiofrequency glow discharge with detection by time-of-flight mass spectrometry (pulsed rf-GD-TOFMS) is investigated for depth profile analysis of self-assembled metallic nanostructures. Two types of nanostructured materials were successfully studied: self-assembled NAA templates filled with arrays of single metallic nanowires of Ni as well as arrays of multilayered Au/FeNi/Au and Au/Ni nanowires and nanotubular titanium dioxide templates filled with Ni nanowires, proving that pulsed rf-GD-TOFMS allows for fast and reliable depth profile analysis as well as for the detection of contaminants introduced during the synthesis process. Moreover, ion signal ratios between elemental and molecular species (e.g., (27)Al(+)/(16)O(+) and (27)Al(+)/(32)O(2)(+)) were utilized to obtain valuable information about the filling process and the presence of possible leaks in the system.