The formation of self-aligned titania and zirconia nanotubes is achieved by the anodisation of Ti and Zr in a fluorine contained electrochemical bath. The anodic oxidation was performed at 30 V for 60 min in a two-electrode glycerol (15% water) bath containing varying amount of NH4F. Despite the fact that a self-aligned nanotubular structure is formed on both titanium and zirconium, the dimensions of zirconia and titania nanotubes are different under the same anodisation parameters. It appears that by using 30 V as the anodisation voltage, the diameter of zirconia nanotubes (30-60 nm) is much smaller compared to that of titania nanotubes (80-100 nm). The length of zirconia nanotubes in the bath consisting of 0.7 g NH4F is 3 µm whereas titania nanotubes formed in the same bath have a length of ~700 nm. The fundamental difference between the nanotubes formed on titanium and zirconium may be related to the rate of oxidation, initial oxide formation during anodisation, pits formation and rate of pits growth for pores formation and stabilisation. Moreover, investigation on the crystallinity of the nanotubes reveals that titania nanotubes are weakly crystalline with crystallite sizes of <5 nm. Whereas, zirconia nanotubes are much more crystalline in cubic modification. The stabilisation of the high temperature phase is thought to originate from the size of the nanotubes walls and the deficiency in oxygen during the growth of the anodic oxide by anodisation.