An innovative procedure has been devised for the processing of X-ray diffraction data from thin films and layered samples, using the conventional Bragg-Brentano geometry. Conventional phase analysis procedures always consider the sample as a homogeneous set of crystals with random orientation; this assumption can lead to severe errors when studying layered samples with thickness less than the penetration depth of the X-rays. Two effects have been considered : the transparency of the layers, that limits the diffracted intensity, and the absorption of the outer layers, that reduces both the incident and the diffracted intensity. Both effects can be described by functions connecting the layer thickness and the absorption coefficient of the present phases to the total diffracted intensity. Adopting this strategy, the thickness of each layer and its phase composition can be refined together with the other structural parameters of interest, such as lattice parameters, crystallite size, microstrain and preferred orientation. The methodology has been tested on samples obtained by physical vapor deposition and by thermal oxidation of metal surfaces.