Cobalt wires have been synthesized by electrodeposition in porous polycarbonate membranes with a pore diameter of ≈200nm and a thickness of ≈6μm. The influence of the citrate concentration, and different substrates (Ag, Cu), sputtered on the bottom of membranes, on the nanocrystalline structure and magnetic properties of the wires are discussed. Crystallization of the wires as a function of the synthesis bath conditions was measured by X-ray diffraction and the magnetic properties at room temperature were measured using vibrating-sample magnetometry. Differences, on deposition rate and crystalline domains size, have been observed, as well as the coercive forces and the hysteresis squareness change in the hysteresis loops of the wires depending on the citrate concentration in the electrochemical bath.