Replacing rare-earth materials in current permanent magnets is a real scientific, economic and environmental challenge. Ferromagnetic 3d transition metals seem an apt direction to go in this field, due to their high residual magnetization and thermal stability. In order to improve their coercive behavior, nanostructured magnets based on the assembly of high-aspect-ratio nanoparticles (i.e. cobalt based nanorods and nanowires) have recently been proposed. In these, the nanoparticle morphology itself drives the magnetization reversal mechanism. This purely geometrical effect seems to obscure the effects of structural defects, although it is clear that high magnetocrystalline energy is required to maintain a stable orientation of the magnetic moment inside the nanoparticles. We present here an experimental study whose aim is to distinguish the role of the stacking faults from the effects of shape and morphology on the magnetization reversal mechanism in cobalt-based nanowires. Coercive field results have been obtained on Co 80 Ni 20 nanowires synthesized by a polyol process. Through accurate control of shape and morphology, it was possible to discard the effects of shape and thus to highlight the influence of crystal defects on the magnetism of Co 80 Ni 20 nanowires. A micromagnetic study, consistent with the experimental analyses, is also presented. The results discussed in this work clearly show that even if the morphological characteristics are conducive to a high coercive field, the presence of numerous stacking faults has the opposite effect and leads to materials with a significantly lower coercive field than expected, which is therefore not suitable for permanent magnet applications.