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An optical and morphological study has been carried out to understand the role of intrinsic defects in the optical properties of opal-based photonic crystals. By doping poly(methylmethacrylate) (PMMA) thin-film opals with larger polystyrene (PS) spheres, structural disorder has being generated perturbing the PMMA matrix periodicity. It is shown that this disorder dramatically affects the optical response of the system worsening its photonic properties. It has been found that the effect of doping is highly dependent not only on the concentration but also on the relative size of the dopant with reference to the matrix. Through a detailed scanning electron microscopy inspection, the sort of structural defects involved, derived from the different particle size used, has been characterized. A direct relationship between the observed optical response with the different perturbations generated in the lattice has been found. In addition, from this study it can be concluded that it is possible to grow high quality alloyed photonic crystals, exhibiting intermediate photonic properties between pure PMMA and pure PS opals by simple sphere size matching and variation of the relative concentration of both components.