We present the results of the structural analysis of inverse opal photonic crystals by microradian X-ray diffraction. Inverse opals based on different oxide materials (TiO2, SiO2 and Fe2O3) were fabricated by templating polystyrene colloidal crystal films grown by the vertical deposition technique. Our results suggest that most inverse opal films possess dominating twinned face-centered cubic structure accompanied by some fragments of hexagonal close-packed and random hexagonal close-packed structures. The studied samples possessed individual structures with different ratios of the above fragments. By fitting the results of the angular-dependent X-ray diffraction by the Wilson model we estimate the stacking probability α in the studied samples to be ∼ 0.7–0.8. Microradian X-ray diffraction therefore provides detailed structural information on opal-based photonic crystals and can be applied to opaque inverse opals or the samples with a periodicity < 300 nm, whose structure cannot be investigated by conventional optical methods.