Using the combination of electron microscopy and x-ray reflectivity, we have studied the defects at the surface of fatty-acid multilayers and shown that the last deposited layer is poorly filled and quite disordered. This accounts for the large value of the roughness provided by x-ray measurements. Furthermore, a few holes and islands of extra layers are observed; the former are due to wetting problems, whereas the latter result from collapses and crystal growth mechanisms.