We analyse the single-mode transmission of microwaves in a guide with internal random structure. The waveguide contains scatterers characterized by random heights and positions, corresponding to compositional and structural disorder. We measure the effects of cross-correlations between two kinds of disorder, showing how they enhance or attenuate the experimentally found transmission gaps generated by long-range self-correlations. The results agree with the theoretical predictions obtained for the aperiodic Kronig-Penney model and prove that self-and cross-correlations also have relevant effects in finite disordered samples of small size.