Thin films made of weak polyelectrolytes poly(allylamine hydrochloride) (PAH) and poly(acrylic acid) (PAA) have been fabricated on silicon wafers using the layer-by-layer (LbL) method. To study the influence of counteranion type on the growth and properties of PAH/PAA multilayers, the nature of the supporting sodium salt was varied from cosmotropic to chaotropic anions (F-, Cl-, and ClO4 -). Results of ellipsometry and AFM measurements indicate that the film thickness and surface roughness systematically increase on the order F- < Cl- < ClO4 -. Furthermore, we found that the hydrophobicity of the PAH/PAA multilayer also follows the described trend when a polycation is the terminating layer. However, the heating of PAH/PAA multilayers to 60 °C during the LbL assembly suppressed the influence of background anions on the multilayer formation and properties. On the basis of the obtained results, it could be concluded that thermal annealing induces changes at the polymer-air interface in the sense of reorientation and migration of polymer chains.