Nickel and Cobalt nanowires were grown in highly ordered pores of anodic alumina membranes using pulsed electrodeposition. The hexagonally arranged pore matrices were fabricated by self-patterning in two successive anodization processes. Before the filling process, the insulating barrier layer at the bottom of the membrane was thinned homogeneously by current-limited anodization steps. During the deposition from a Watts bath two short millisecond deposition pulses were applied, followed by a comparatively long delay time to attain quite a high metal ion concentration at the deposition interface. This technique yielded completely metal-filled alumina membranes, wich were analyzed by scanning electron microscopy and X-ray diffraction. The magnetic behavior of the metal-filled nano-pore arrays was characterized by SQUID-magnetometer measurements and the coupling between the nanowires was analyzed.