The aim of this investigation was to reveal the processing differences in achieving nanoporous anodized aluminium from aluminium alloys and their application for cobalt nanowires electrodeposition. The following types of aluminium were tested: pure Al (99.99%), and commercial alloys: AA1050, 6082 and 6060. Because of the differences in the surface temperature and high voltages during the anodizing steps, some stresses can be built up in the material. Therefore a strict temperature control should be done to limit thermal stresses in materials. Alloying elements (Si, Mg) cause precipitates that are observed on the surface, especially for 6060 alloy. Nevertheless, a nanoporous structure can be obtained at the end of second anodization step on all aluminium alloys investigated. It was shown that the number density of pores on the surface is practically independent on the aluminium alloys used. However, the degree of hexagonal distribution of the pores depends on the type of anodized aluminium alloy. Also, a successful fabrication of Co nanowire arrays using nanoporous anodic alumina template produced on Al alloy has been demonstrated, and the uniform filling of the template by cobalt nanowires arrays is discussed.