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Anodic aluminum oxide (AAO) films possess vertical cylindrical channels that self-organize into a periodic hexagonal network upon film growth. The degree of pore ordering into a close-packed lattice depends on many experimental parameters such as the electrolyte composition, applied voltage, etc. Recently, the influence of crystallographic orientation of Al substrate on the positional, orientational and longitudinal order of the pores has been found. Nevertheless the mechanism of the self-organization of pores into an ordered hexagonal lattice remains a topic of debate. In the present study the AAO films obtained on single crystal substrates with different crystallographic orientations were quantitative characterized by SAXS technique. The diffraction experiments were performed at the beamline BM26B “DUBBLE” of ESRF. The AAO porous film, grown on Al(111) substrate exhibits a spot-like diffraction pattern with the 6-fold symmetry that corresponds to a distinct decrease in the mosaicity of the hexagonal porous structure. In case of substrate with (100) orientation several rings with uniform distribution of intensity indicate the incompatibility of the 4-fold crystallographic symmetry of the underlying metal crystal and the hexagonal symmetry of the perfect AAO structure. In case of the Al(110) substrate six broad maxima represent an intermediate degree of the in-plane orientational pore ordering. In order to observe the influence of the crystallographic orientation on the longitudinal pore arrangement, a specially designed Al(100) single crystal with the vicinal edges tilted from the (100) plane by 5° was used. It was shown, that the grown direction of AAO channels is tailored by two competing factors: (i) electromigration of ions under external electric field, which push it along the normal to the Al surface; (ii) presence of stable crystal faces of (100) family, crossing of which by the pore is energetically unfavourable due to hampered diffusion of oxygen ions through dense atomic planes. Aforementioned factors lead to coexisting of two preferable pore grown directions in AAO with disorientation of about 0.3°. Moreover, pores growing in different directions during anodization retain hexagonal domains with various in-plane orientations.