We report the synthesis of Co and Fe nanowires and nanotubes electrochemically deposited through nanoporous membranes. Depending upon the pulse electrodeposition parameters, the structure of Co nanowires is either a pure hexagonal phase or a polytype structure related to the stacking of hexagonal and face-centered cubic forms. Similarly, iron nanowires can be prepared with single or multicrystallographic phases. The control of the wire structure was achieved via the overpotential used to initiate growth. Moreover, nanotubes, whose formation could result from a complexation between metal ions and the polymeric membrane, were also directly synthesized.