Molecular orientation within azopolymer thin films is important for their nonlinear optical properties and photonic applications. We have used optical second-harmonic generation (SHG) to study the molecular orientation of Layer-by-Layer (LbL) films of a cationic polyelectrolyte (poly(allylamine hydrochloride)) and an anionic polyelectrolyte containing azochromophore side groups (MA-co-DR13) on a glass substrate. The SHG measurements indicate that there is a preferential orientation of the azochromophores in the film, leading to a significant optical nonlinearity. However, both the signal strength and its anisotropy are not homogeneous throughout the sample, indicating the presence of large orientational domains. This is corroborated with Brewster angle microscopy. The average SHG signal does not increase with film thickness, in contrast to some reports in the literature, indicating an independent orientational order for successive bilayers. Analyzing the SHG signal as a function of the input and output polarizations, a few parameters of the azochromophore orientational distribution can be deduced. Fitting the SHG signal to a simple model distribution, we have concluded that the chromophores have an angular distribution with a slight in-plane anisotropy and a mean polar angle ranging from 45° to 80° with respect to substrate normal direction, with a relatively large width of about 25°. These results show that SHG is a powerful technique for a detailed investigation of the molecular orientation in azopolymer LbL films, allowing a deeper understanding of their self-assembling mechanism and nonlinear optical properties. The inhomogeneity and anisotropy of these films may have important consequences for their applications in nonlinear optical devices.