In this work we investigate the periodic arrangement and crystalline order of Langmuir-Blodgett multilayers of a perylene-3,4,9,10-tetracarboxyldiimide derivative (PTCDI-Opent) and of a long chain ammonium salt of 12-phosphomolybdate (PMo12O403-) deposited on (111)-oriented Si substrates by X-ray specular reflectivity (XSR) and grazing incidence X-ray diffraction measurements (GIXD), This is the first experimental study of the structural order performed on these complex compounds, Our results show that both films are quite uniform in thickness as demonstrated by well defined Kiessig fringes collected in the XSR spectra. The presence of sharp specular Bragg peaks in the XSR measurements of the PMo12O403-, film indicates a very good crystalline order in the growth direction, For the PTCDI-Opent structure, an unexpected molecular reorganization in the film along the growth direction is found if compared to the molecular conformation at the air-water interface and the transfer ratios. Both films can be identified as monophasic structures, Moreover, the in-plane structural arrangement derived by GIXD shows domains of 70-140 Angstrom lateral size.